Information on EC 3.1.26.4 - ribonuclease H

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY
3.1.26.4
-
RECOMMENDED NAME
GeneOntology No.
ribonuclease H
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
random endonucleolytic cleavage
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
active site residues are Asp10, Gu48, Asp70, His124, Asp134
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
active site structure, substrate binding groove, molecular mechanism for specific RNA*DNA hybrid substrate recognition, binding, and cleavage, a general nuclease activity is necessary for catalysis
O29634
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
Asp10 is critical for activity and involved in binding of divalent metal ion
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
Asp10, Glu48, Asp70, and Asp134 are involved in catalysis, role of Mn2+ in catalysis, mechanism
P0A7Y4
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
Asp149 is essential for catalytic activity, Asp7, Glu8 and Asp112 are invovled in metal ion binding
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
structure-function relationship, a 42 amino acid noncanonical spacer domain is essential for enzyme function, the nuclear localization domain is not required for function but for RNA binding, it modulates the enzyme manganese-dependent activity
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
the catalytic reaction requires 4 acidic residues, catalytic center and catalytic mechanism of type 1 and type 2 ribonucleases, type 1 enzyme requires a histidine as general base, while type 2 enzyme does not, substrate binding of type 2 enzyme
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
active site and substrate binding site structures
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
active site residues D10, E48, D70, and D134 are involved in metal ion binding, overview
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
evolutionary conserved flexible regions are important for catalysis, structure function relationship, enthalpic/entropic compensation mechanism, overview
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
substrate structure influence on enzyme activity, substrate binding, overview
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
the enzyme performs a two-metal catalysis, with metal A activating the nucleophile and metal B stabilizing the transition state, mechanism and structures, overview
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
four acidic active-site residues of Bst-RNase HIII: Asp97, Glu98, Asp202, and Glu232, substrate binding and site structure, active site structure and reaction mechanism, overview
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
possible mechanisms for the RNase HII-catalysed reaction consistent with the pH-dependent behaviour of the enzyme, the active sites of RNase H enzymes contain a cluster of four strictly conserved carboxylate groups, requirement for ionisation of an active site carboxylic acid for metal ion binding or correct positioning of metal ion in the enzyme-substrate complex and a role for a second active site carboxylate in general base catalysis
-
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
active site geometry suggests a two-metal ion-dependent catalytic mechanism
Q9CWY8
endonucleolytic cleavage to a 5'-phosphomonoester
show the reaction diagram
in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low. If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
endoribonuclease H
-
-
-
-
hybrid nuclease
-
-
-
-
hybrid ribonuclease
-
-
-
-
hybridase
-
-
-
-
hybridase (ribonuclease H)
-
-
-
-
nuclease, hybrid ribo-
-
-
-
-
nuclease, ribo-, H
-
-
-
-
P32
-
-
-
-
ribonuclease H
-
-
-
-
RNA*DNA hybrid ribonucleotidohydrolase
-
-
-
-
RNase H
-
-
-
-
RNase H1
-
-
-
-
RNase HI
-
-
-
-
RNase HII
-
-
-
-
RNase HIII
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9050-76-4
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Aeropyrum pernix DSM 11879
-
SwissProt
Manually annotated by BRENDA team
type 2 enzyme
Uniprot
Manually annotated by BRENDA team
a large-MW enzyme form and a small-MW enzyme form; calf
-
-
Manually annotated by BRENDA team
calf; ribonuclease H IIa
-
-
Manually annotated by BRENDA team
different splicing variants
-
-
Manually annotated by BRENDA team
strain AR39, RNases HII and HIII, encoded in ORFs CP0654 and CP0782
-
-
Manually annotated by BRENDA team
Chlamydia pneumoniae AR39
-
-
-
Manually annotated by BRENDA team
Chlamydia pneumoniae AR39
strain AR39, RNases HII and HIII, encoded in ORFs CP0654 and CP0782
-
-
Manually annotated by BRENDA team
one Mn2+-dependent RNase H and one Mg2+-dependent RNase H; strain GD-2
-
-
Manually annotated by BRENDA team
strain GD-2
-
-
Manually annotated by BRENDA team
Daucus carota GD-2
strain GD-2
-
-
Manually annotated by BRENDA team
gene rnhB
SwissProt
Manually annotated by BRENDA team
gene rnhb, type 2 enzyme, wild-type DY330 and knock-out strain
-
-
Manually annotated by BRENDA team
strain B and strain D110
-
-
Manually annotated by BRENDA team
strain HB101
-
-
Manually annotated by BRENDA team
type 1 enzyme
Uniprot
Manually annotated by BRENDA team
type 1 enzyme
-
-
Manually annotated by BRENDA team
type II enzyme, gene rnhB
-
-
Manually annotated by BRENDA team
one Mn2+-dependent RNase H and one Mg2+-dependent RNase H
-
-
Manually annotated by BRENDA team
Halobacterium salinarum NRC-1
-
UniProt
Manually annotated by BRENDA team
isoform RNase H2
-
-
Manually annotated by BRENDA team
RNase H1 is a type 2 enzyme
-
-
Manually annotated by BRENDA team
subunit H2B; isoform RNase H2
UniProt
Manually annotated by BRENDA team
subunit H2C; isoform RNase H2
UniProt
Manually annotated by BRENDA team
type 1 and type 2 enzymes
-
-
Manually annotated by BRENDA team
type 1 enzyme
-
-
Manually annotated by BRENDA team
type 2 enzyme
-
-
Manually annotated by BRENDA team
single copy gene, 3 isozymes A, B, and C of the type II enzyme
SwissProt
Manually annotated by BRENDA team
single copy gene, 3 isozymes A, B, and C of the type II enzyme
SwissProt
Manually annotated by BRENDA team
4 enzyme form: HA1, HA2, HB1 and HB2
-
-
Manually annotated by BRENDA team
gene rnaseh1
-
-
Manually annotated by BRENDA team
bifunctional protein, the N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase CobC
UniProt
Manually annotated by BRENDA team
bifunctional protein, the N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase CobC
UniProt
Manually annotated by BRENDA team
gene PAB0352
-
-
Manually annotated by BRENDA team
type 2 enzyme
-
-
Manually annotated by BRENDA team
ribonuclease H2
-
-
Manually annotated by BRENDA team
ribonuclease HA
-
-
Manually annotated by BRENDA team
strains JB740 and yEB104A
-
-
Manually annotated by BRENDA team
type 2 enzyme
-
-
Manually annotated by BRENDA team
Saccharomyces cerevisiae W-303
-
-
-
Manually annotated by BRENDA team
strain SIB1, psychrotrophic bacterium, gene rnhB
SwissProt
Manually annotated by BRENDA team
strain SIB1, psychrotrophic bacterium, gene rnhB
SwissProt
Manually annotated by BRENDA team
Sulfolobus tokodaii 7
-
SwissProt
Manually annotated by BRENDA team
strain GI, enzyme form: H-1, H-2 and H-3
-
-
Manually annotated by BRENDA team
Tetrahymena pyriformis GI
strain GI, enzyme form: H-1, H-2 and H-3
-
-
Manually annotated by BRENDA team
type 2 enzyme
-
-
Manually annotated by BRENDA team
Thermotoga maritima DSM 3109
-
UniProt
Manually annotated by BRENDA team
Thermovibrio ammonificans DSM 15698
-
UniProt
Manually annotated by BRENDA team
strain HB8
-
-
Manually annotated by BRENDA team
strain HB8, type I enzyme, gene rnhA
-
-
Manually annotated by BRENDA team
thermophilic enzyme
-
-
Manually annotated by BRENDA team
type I enzyme
-
-
Manually annotated by BRENDA team
clone VP62
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
Q9CWY8
mutations in each of the three RNase H2 subunits are implicated in a human auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
physiological function
Q9CWY8
ribonuclease H2 is the major nuclear enzyme involved in the degradation of RNA/DNA hybrids and removal of ribonucleotides misincorporated in genomic DNA
physiological function
-
RNase H1 is an indispensable protein for Okazaki fragment processing in human mtDNA replication
physiological function
-
RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutieres syndrome, a severe autoimmune disorder
physiological function
-
RNase H2 junction recognition is important for the removal of RNA embedded in DNA and may play an important role in DNA replication and repair
physiological function
-
RNase HIII-type ribonucleases are members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are possibly be involved in DNA replication and repair
physiological function
-
both Pf-RNase HII and Pf-FEN-1 are required for the effective processing of an Okazaki substrate
physiological function
O29634
the enzyme is involved in RNA primer removal during DNA replication
physiological function
-
ribonucleotide excision repair is most efficient when the ribonucleotide is incised by RNase H2. RNase H1 fails to substitute for RNase H2 in the incision step of ribonucleotide excision repair
physiological function
-
RNase H is essential for foamy viral protease activity
physiological function
-
RNase H2 is implicated in the processing of the 5' ends of Okazaki fragments. RNase H2 also links DNA replication and DNA repair through ribonucleotide excision repair. The RNase H2 interaction network also functions to suppress genome instability
physiological function
-
RNase HI stimulates the activity of RnlA toxin
physiological function
-
RNase HIII-type ribonucleases are members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are possibly be involved in DNA replication and repair
-
malfunction
-
strains deficient in RNase H2 display a weak mutator phenotype which is consistent with a defect in DNA repair. RNase H2 defects cause alterations in the timing of cell cycle transitions
additional information
-
RNase H exists as a free enzyme
additional information
Q9X122
the C-terminal RNase H domain loses the ability to suppress the RNase H deficiency of an Escherichia coli rnhA mutant, the hybrid binding domain is responsible for in vivo RNase H activity
additional information
-
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+. Residue Y163 is important for binding of both (5')RNA-DNA(3') junctions and RNA/DNA substrates
additional information
-
the RNase HII contains a regulatory C-terminal tail. The C-terminus might form a short alpha-helix in which two residues, I195 and L196, are essential for the cleavage activity. The C-terminal alpha-helix is likely involved in the Mn2+-dependent substrate cleavage activity through stabilization of a flexible loop structure. Structure and function of both archaeal RNase HII, overview
additional information
Q9CWY8
the RNASEH2A C-terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer
additional information
-
the substrate binding site is located in the N-terminal TBP-like domain of RNase H3. The N-terminal domain of RNase H3 uses the flat surface of the b-sheet for substrate binding as TBP to bind DNA. This domain may greatly change conformation upon substrate binding
additional information
-
the type 2 RNase H is an Mg2+- and alkaline pH-dependent enzyme
additional information
-
translation initiates at each of the two in-frame AUGs of the Rnaseh1 mRNA, with the longer form being imported into mitochondria, regulation mechanisms, modelling, overview
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Thermotoga maritima DSM 3109
Q9X017
-
-
-
?
12 basepair DNA-DNA duplex + H2O
?
show the reaction diagram
Q6L6Q4
oligomeric substrate, cleavage at multiple sites, product identification
-
-
?
12bp-RNA-DNA hybrid + H2O
?
show the reaction diagram
Chlamydia pneumoniae, Chlamydia pneumoniae AR39
-
RNase HII cleaves the 12 bp RNA-DNA substrate at multiple sites, but RNase HIII at only one site
-
-
?
29 basepair DNA-RNA-DNA/DNA + H2O
?
show the reaction diagram
Q6L6Q4
oligomeric substrate, cleavage mainly in the middle of the tetraribonucleotide, product identification
-
-
?
35 bp DNA-RNA-DNA/DNA chimeric hybrid + H2O
?
show the reaction diagram
Chlamydia pneumoniae, Chlamydia pneumoniae AR39
-
-
-
-
?
5'-(6-carboxy-fluorescein)-cggagaugacgg-3'/5'-CCGTCTCTCCG-3' + H2O
?
show the reaction diagram
Aeropyrum pernix, Aeropyrum pernix DSM 11879
Q9YET5
the enzyme cleaves 12-bp RNA/DNA at multiple sites between the 3rd and 11th residues, but most preferentially at c10g11 and less preferentially at g5a6 and u7g8. The cleavage pattern of Mg2+-dependent activity is the same as that of Co2+-dependent activity, but different from that of Mn2+-dependent activity
-
-
?
D13-R4-D12-D29 hybrid + H2O
?
show the reaction diagram
Q9X122
-
-
-
?
D14R1D3:DNA18 + H2O
?
show the reaction diagram
Q9CWY8
-
-
-
?
DNA*DNA + H2O
?
show the reaction diagram
-
5'-to 3'-exonuclease activity, degradation of DNA*DNA duplexes
-
-
?
DNA-(1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-(2'-alkoxy-1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-(aza-ENA-T)-antisense-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-(azetidine-T)-antisense-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-(oxetane-T)-antisense-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-2'-methoxyethoxy RNA hybrid
?
show the reaction diagram
-
chimeric substrates containing a central DNA region with flanking northern-biased 2'-methoxyethyl nucleotides hybridized to complementary RNA, enhanced cleavage rates are observed for the eastern-biased 2'-ara-fluorothymidine and bulge inducing N-methylthymidine modifications positioned at the 5'-DNA/3'-MOE junction as well as the southern-biased 2'-methylthiothymidine and conformationally flexible tetrafluoroindole modifications positioned at the 5'-MOE/3'-DNA junction, overview
-
-
-
DNA-2'-methoxyethoxy-antisense RNA hybrid + H2O
?
show the reaction diagram
-
2'-methoxyethoxy nucleotides, positioned at the 3' and 5' poles, into the antisense oligodeoxyribonucleotide of the heteroduplex to alter the helical geometry of the substrate
-
-
?
DNA-rN1-DNA/DNA + H2O
?
show the reaction diagram
-
specific cleavage by RNase HII at the 5'-side of the ribonucleotide, cleavage efficiencies of the perfectly matched DNA-rN1-DNA/DNA duplexes are higher than those carrying a mismatched ribonucleotide
-
-
?
DNA-RNA duplex + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-RNA duplex + H2O
?
show the reaction diagram
-
specific cleavage of the RNA part
-
-
?
DNA-RNA duplex + H2O
?
show the reaction diagram
-
the enzyme cleaves RNA exclusively in a DNA-RNA heteroduplex, cleavage pattern and site specificity dependent on the substrate structure, overview
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
Q9KEI9
-
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
P10442
-
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
Q25C12
-
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
-
RNase HII specifically catalyses the hydrolysis of phosphate diester linkages contained within the RNA portion of DNA/RNA hybrids, usage of 5'-fluorescent oligodeoxynucleotide substrates
-
-
?
DNA-RNA hybrid + H2O
?
show the reaction diagram
Q25C12
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
Q6L6Q4
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
strategy for regulating RNA digestion by RNase H by using a light-activated DNA hairpin, overview
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
Q6L6Q4
3H-labeled M13 DNA/RNA hybrid substrate, the N-terminal domain and C-terminal helix are involved in substrate binding, but the former contributes to substrate binding to a higher extent than the latter, overview
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
poly-rA/poly-dT substrate, RNase H1 contains an N-terminal domain termed dsRHbd or hybrid binding domain for binding both dsRNA and RNA/DNA hybrid, the RNA strand is recognized by a protein loop, which forms hydrogen bonds with the 2'-OH groups, substrate recognition and binding structure, residues, Y29, R32, R33, W43, R57, K59, K60, R72, and K73 are involved, overview
determination of reaction products with less than 20-nucleotides
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
RNase H binds RNA-DNA hybrid and double-stranded RNA duplexes with similar affinity, but only cleaves the RNA in the former in a specific manner, substrate recognition, overview
-
-
?
DNA-RNA hybrid + H2O
ssDNA + 5'-phosphomonoester oligonucleotides
show the reaction diagram
-
in the pause of minus strang synthesis, RNAse H degrades the RNA template, with the exception of the polypurine tract sequence, immediately upstream of U3, which serves as a primer for plus-strand synthesis
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
show the reaction diagram
-
preference for RNA-DNA hybrid but low activity towards ss and ds RNA and DNA, most active substrate: (rA)n-(dT)n
-
?
DNA-RNA-DNA hybrid + H2O
?
show the reaction diagram
-
specific hydrolysis of the RNA strand of the hybrid
-
-
?
DNA-RNA-DNA/DNA hybrid + H2O
?
show the reaction diagram
Q9X017
a duplex containing a (5')RNA-DNA(3') junction with one, three, or six ribonucleotides, i.e. DNA5-RNA1-DNA6/DNA12, DNA3-RNA3-DNA6/DNA12, and RNA6-DNA6/DNA12, and a substrate with a (5')DNA-RNA(3') junction, DNA5-RNA7/DNA12
-
-
?
DNA12-RNA1-DNA27/DNA40 hybrid + H2O
?
show the reaction diagram
Q5TBB1, Q8TDP1
-
enzyme cleaves RNA20/DNA20 hybrid and DNA12-RNA1-DNA27/DNA40 hybrid substrates with similar efficiency
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
show the reaction diagram
-
enzyme excises misincorporated ribonucleotides in DNA
-
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
show the reaction diagram
-
enzyme excises misincorporated ribonucleotides in DNA, enzyme places the first 5' nick, while the second 3' cut is made by FEN-1 protein
-
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
show the reaction diagram
-
preferred substrate, enzyme excises misincorporated ribonucleotides in DNA
-
-
?
dsDNA oligonucleotide with a stretch of ribonucleotides + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
show the reaction diagram
-
enzyme excises misincorporated ribonucleotides in DNA
-
-
?
dsDNA oligonucleotides with a single ribose + H2O
dsDNA oligonucleotides with 1 nt gap + 5'-monophosphate ribonucleotide
show the reaction diagram
-
preferred substrate, enzyme excises misincorporated ribonucleotides in DNA, enzyme places the first 5' nick, while the second 3' cut is made by Rad27p
-
-
?
M13 DNA-RNA hybrid + H2O
?
show the reaction diagram
Q6L6Q4
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
show the reaction diagram
P10442
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
show the reaction diagram
Q25C12
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
show the reaction diagram
-
the enzyme degrades the RNA moiety of the heteroduplex
-
-
?
M13 DNA-RNA hybrid + H2O
?
show the reaction diagram
Q25C12
-
-
-
?
M13 DNA/RNA hybrid + H2O
?
show the reaction diagram
Q9X122
-
-
-
?
peptide nucleic acid - 2'-deoxy 2'-fluoroarabinonucleic acid hybrid + H2O
?
show the reaction diagram
-
chimeric oligomers possessing a single central peptide nucleic acid insert are capable of forming hybrid duplexes with complementary RNA, although with diminished thermal stability in comparison to the unmodified oligomers
-
-
?
peptide nucleic acid - DNA + H2O
?
show the reaction diagram
-
chimeric oligomers possessing a single central peptide nucleic acid insert are capable of forming hybrid duplexes with complementary RNA, although with diminished thermal stability in comparison to the unmodified oligomers
-
-
?
poly(rA)/poly(dT) + H2O
?
show the reaction diagram
Q9X017
-
-
-
?
poly-rA/poly-dT + H2O
?
show the reaction diagram
Q5TBB1, Q8TDP1
-
products are short oligonucleotides with very few intermediate-sized oligonucleotides
-
?
polyA*dT36 hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
PPT-RNA + H2O
?
show the reaction diagram
-
single-stranded, the DNA-linked enzyme mutant shows highly reduced activity compared to the wild-type enzyme, specific cleavage of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA
-
-
?
RNA + H2O
?
show the reaction diagram
Sulfolobus tokodaii, Sulfolobus tokodaii 7
-
the enzyme cleaves the RNA strand of an RNA/DNA hybrid or an RNA/RNA duplex in the presence of Mn2+ or Co2+
-
-
?
RNA*2'F-ANA-DNA hybrid + H2O
?
show the reaction diagram
-
cleaves the RNA portion of hybrid duplexes of butyl-modified 2'F-ANA-DNA oligonucleotides containing acyclic interresidue units with complementary RNA
-
-
?
RNA*antisense-DNA hybrid + H2O
?
show the reaction diagram
-
cleaves the RNA portion of hybrid duplexes of modified antisense DNA oligonucleotides containing acyclic interresidue units with complementary RNA
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
very low activity
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
specific for
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
cleaves the RNA portion
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
P0A7Y4
12 bp and 29 bp oligomers, cleavage site specificity depends on bound metal ion, wild-type end mutant enzymes
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
enzyme is active only under reducing conditions, wild-type enzyme and deletion mutant H1[DELTA1-73] are inactive under oxidizing conditions
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
hydrolyses the RNA strang of the RNA*DNA heteroduplex
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
specific for the RNA moiety
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
the C-terminal domain of type 2 enzyme is involved in the interaction with the substrate
-
-
?
RNA*DNA hybrid + H2O
5'-phospho-3'-hydroxyoligonucleotides
show the reaction diagram
-
specifically degrades the RNA moiety
-
-
?
RNA*DNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
5'-to 3'-exonuclease activity, degradation of RNA*DNA duplexes
-
-
?
RNA-DNA duplex + H2O
?
show the reaction diagram
Q8U036
-
-
-
?
RNA-DNA duplex + H2O
?
show the reaction diagram
Q8EE30
-
-
-
?
RNA-DNA duplex + H2O
?
show the reaction diagram
P9WLH5
substrate both for full-lentgh enzyme and isolated RNase H N-terminal RNase H domain
-
-
?
RNA-DNA heteroduplex + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
a mixture of oligoribonucleotides with 5'-phosphate and 3'-hydroxyl terminus
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
a mixture of oligonucleotides with 5'-phosphate termini and only a minor proportion of 5'-mononucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
oligonucleotides and a small amount of mononucleotides which possess 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
can degrade about 90% of the RNA strand of and RNA-DNA hybrid
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
hybrid between viral f1 and its complementary RNA, slight preference for cleavage adjacent to pyrimidine
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
isoenzyme C-1 and C-2 specifically act on the RNA moiety of RNA-DNA hybrid, isoenzyme C-3 degrades single-stranded RNA as well as the RNA of hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
the enzyme can hydrolyze a DNA*RNA*DNA/DNA heteroduplex that contains a single ribonucleotide
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
phiX174DNA-RNA
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
T7 DNA-RNA hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rCdG)
mixture of oligonucleotides, ranging in size from dinucleotides to larger than hexanucleotides. No mononucleotides can be detected
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
digestion of more than 95% of the RNA in RNA-DNA hybrids to acid-soluble products
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
DNA-RNA hybrid made from phage f1 DNA
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
DNA-RNA hybrid made from phage f1 DNA
the bulk of the resulting poly(dA) obtained by cleavage of poly(dT)*poly(A4)-(dA)x still retains one covalently linked riboadenylic acid end group, a small portion carries a ribo dinucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
hybrid obtained by transcription of calf thymus DNA
oligoribonucleotides with 3'-OH and 5'-phosphate ends
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
deoxyribotetranucleotides can still be cleaved
the bulk of the resulting poly(dA) obtained by cleavage of poly(dT)*poly(A4)-(dA)x still retains one covalently linked riboadenylic acid end group, a small portion carries a ribo dinucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
M13 DNA:RNA[P*]DNA
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(dCrI)
oligoribonucleotides with a chain length of less than 15, having 5'-phosphate and 3'-hydroxyl end group, oligonucleotides of chain length 6-14, no mononucleotides formed
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
degrades only an RNA chain hydrogen bonded to DNA
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
M13 DNA/RNA hybrid
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rUdA)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rUdA)
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rUdA), poly(rCdI)
5'-phosphorylated oligonucleotides
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
oligoribonucleotides with a chain length of less than 15, having 5'-phosphate and 3'-hydroxyl end group, oligonucleotides of chain length 6-14, no mononucleotides formed
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
mixture of oligonucleotides, ranging in size from dinucleotides to larger than hexanucleotides. No mononucleotides can be detected
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
a mixture of oligoribonucleotides with 5'-phosphate and 3'-hydroxyl terminus
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
oligonucleotides of various chain length, mainly 3-9 nucleotides in length
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
oligonucleotides with 3'-hydroxyl and 5'-phosphate termini with the structure (pA)3-9 are formed from poly(A)*poly(dT)
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
oligoribonucleotides + monoribonucleotides terminated by a 5'-phosphate
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
5'-phosphorylated oligonucleotides
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rAdT)
oligoribonucleotides with 3'-OH and 5'-phosphate ends
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(dT)'poly(A) in the presence of Mg2+ is the best substrate, poly(dC)'poly(G) is attacked much more slowly. Degradation velocity rises with the increasing length of the deoxyribo strand. The efficieny decreases in the following order: (dA)4-poly(U), (dG)4*poly(C), (dC)4*poly(G), (dT)4*poly(A)
the bulk of the resulting poly(dA) obtained by cleavage of poly(dT)*poly(A4)-(dA)x still retains one covalently linked riboadenylic acid end group, a small portion carries a ribo dinucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
RNase H2 incises the DNA 5'-of the ribonucleotide, generating DNA containing 3'-hydroxyl and 5'-phosphoribonucleotide ends
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
Daucus carota GD-2
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
Daucus carota GD-2
-
poly(rAdT)
a mixture of oligoribonucleotides with 5'-phosphate and 3'-hydroxyl terminus, oligonucleotides of various chain length, mainly 3-9 nucleotides in length
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
Tetrahymena pyriformis GI
-
-
oligonucleotides and a small amount of mononucleotides which possess 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
-
the enzyme may play a role in ribonucleotide excision from genomic DNA during replication
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
-
the enzyme could be involved in the removal of RNA primers during DNA replication
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
Thermovibrio ammonificans, Thermovibrio ammonificans DSM 15698
E8T217
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
P03355
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
A1Z651
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Q9HSF6
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
E0X765
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
O67644
the enzyme specifically cleaves the RNA strand of RNA/DNA hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Saccharomyces cerevisiae W-303
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Chlamydia pneumoniae AR39
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Halobacterium salinarum NRC-1
Q9HSF6
-
-
-
?
RNA-DNA hybrid HTS-1 + H2O
?
show the reaction diagram
A1Z651
5'-GAUCUGAGCCUGGGAGCU-fluorescein-3' annealed to 5'-Dabcyl-AGCTCCCAGGCTCAGATC-3'
-
-
?
RNA-DNA hybrid HTS-2 + H2O
?
show the reaction diagram
A1Z651
5'-CUGGUUAGACCAGAUCUGAGCCUGGGAGCU-fluorescein-3' annealed to 5'-Dabcyl-AGCTCCCAGGCTCAGATC-3'
-
-
?
RNA-DNA single-stranded chimera + H2O
?
show the reaction diagram
O29634
-
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
show the reaction diagram
-
enzyme removes RNA primers from lagging strand fragments during DNA replication, 5'-to 3'-exonuclease activity, degradation of the RNA portion of the duplex
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
show the reaction diagram
O29634
RNA primer recognition and removal during DNA replication
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
show the reaction diagram
-
specific removal of the RNA portion of the duplex
-
-
?
RNA-DNA*DNA hybrid + H2O
8mer oligonucleotide
show the reaction diagram
O29634
7 M urea-denatured 18mer, no activity with untreated hybrid, specific removal of the RNA portion of the duplex
-
-
?
RNA-DNA*DNA hybrid + H2O
oligonucleotides
show the reaction diagram
O29634
7 M urea-denatured 37mer, no activity with untreated hybrid, specific removal of the RNA portion of the duplex
a 20mer, a 10mer, a 9mer, and a 7mer
-
?
RNA-DNA/DNA hybrid + H2O
?
show the reaction diagram
-
PabRNase HII acts as a specific endonuclease on RNA-DNA/DNA duplexes. Specific cleavage, one nucleotide upstream of the RNA-DNA junction, occurs on a substrate in which RNA initiators is fully annealed to the cDNA template. Additionally, PabRNase HII cleaves a single ribonucleotide embedded in a double-stranded DNA
-
-
?
RNA-RNA duplex + H2O
?
show the reaction diagram
Q8U036
reaction occurs in presence of Mn2+-ions. Residues D110, R113 and F114 are responsible for the activity, the residues are located in the region that discriminates DNA from RNA in the non-substrate strand of the duplexes
-
-
?
RNA-RNA duplex + H2O
?
show the reaction diagram
P9WLH5
substrate both for full-lentgh enzyme and isolated RNase H N-terminal RNase H domain
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
F9VN79
-
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
Q9X017
an RNA/DNA hybrid (RNA12/DNA12)
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
O29634
model Okazaki fragment 18-mer RNA-DNA/DNA substrate (Q18), RNase H is a structure-specific endonuclease, it cleaves the 25-bp RNA/DNA hybrid at multiple sites, indicating that the enzyme cleaves RNA/DNA in a sequence-independent manner. In the absence of complementary DNA, the chimeric RNA-DNA strand is not cleaved by the enzyme
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
Sulfolobus tokodaii 7
F9VN79
-
-
-
?
RNA18:DNA18 + H2O
?
show the reaction diagram
Q9CWY8
-
-
-
?
RNA20/DNA20 hybrid + H2O
?
show the reaction diagram
Q5TBB1, Q8TDP1
-
enzyme cleaves RNA20/DNA20 hybrid and DNA12-RNA1-DNA27/DNA40 hybrid substrates with similar efficiency
-
?
single-stranded RNA + H2O
?
show the reaction diagram
-
isoenzyme C-1 and C-2 specifically act on the RNA moiety of RNA-DNA hybrid, isoenzyme C-3 degrades single-stranded RNA as well as the RNA of hybrids
-
-
?
ssDNA-dsDNA + H2O
?
show the reaction diagram
-
5'-to 3'-exonuclease activity, exonuclease activity removing short oligonucleotides of 3-30 nucleotides from adjacent DNA
-
-
?
ssRNA + H2O
?
show the reaction diagram
-
-
-
-
?
M13 DNA/RNA hybrid + H2O
?
show the reaction diagram
-
substrate is 3H-labeled M13 DNA/RNA hybrid
-
-
?
additional information
?
-
O29634
cleavage specificity
-
-
-
additional information
?
-
-
substrate specificity
-
-
-
additional information
?
-
-
the enzyme lacks double-stranded and single-stranded RNase and DNase activities. No hydrolysis of the DNA moiety of the RNA/DNA heteroduplex
-
-
-
additional information
?
-
-
no degradation of single stranded RNA
-
-
-
additional information
?
-
-
ribonuclease H(70) possesses cryptic reverse transcriptase activity
-
-
-
additional information
?
-
-
no attack of ribosomal RNA
-
-
-
additional information
?
-
-
no activity on natural double-stranded or single-stranded DNA, or on single-stranded RNA
-
-
-
additional information
?
-
-
the enzyme cannot cleave the phosphodiester bond covalently linking ribonucleotides to DNA
-
-
-
additional information
?
-
-
regulation
-
-
-
additional information
?
-
-
presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
-
-
-
additional information
?
-
-
the enzyme is regulated by a unique redox switch formed by adjacent Cys147 and Cys148, formation of a disulfide bond, under oxidizing conditions, between Cys147 and Cys148 results in an inactive enzyme conformation
-
-
-
additional information
?
-
-
no activity with dT36 and polyA
-
-
-
additional information
?
-
-
substrate characterization and substrate specificity
-
-
-
additional information
?
-
-
substrate characterizationa and substrate specificity
-
-
-
additional information
?
-
-
substrate specificity, enzyme plays a role in the repair of misincorporated ribonucleotides rather than or in addition to processing RNA*DNA hybrid molecules
-
-
-
additional information
?
-
Q8WR57
the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
-
-
-
additional information
?
-
Q8WSZ0
the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
-
-
-
additional information
?
-
-
no activity with a DNA or a RNA duplex
-
-
-
additional information
?
-
-
stage-specific expression of RNAse H1 isozymes with different substrate specificities and divalent cation requirements, claevage specificties, overview
-
-
-
additional information
?
-
P10442
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
-
additional information
?
-
Q25C12
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
-
additional information
?
-
-
design of a light-activated DNA hairpin to control the RNase H-mediated hydrolysis of mRNA, overview
-
-
-
additional information
?
-
-
determination of RNase H cleavage potential of the RNA strand basepaired with the complementary antisense oligonucleotides containing North-East conformationally constrained 1',2'-methylene-bridged azetidine-T and oxetane-T nucleosides, North-constrained 2',4'-ethylene-bridged aza-ENA-T nucleoside, and 2'-alkoxy modified nucleosides, i.e. 2'-O-Me-T and 2'-O-MOE-T modifications, molecular dynamics, overview
-
-
-
additional information
?
-
-
development of a CpRNase HII-based method for activity assay and detection: DNA-rN1-DNA fragments are modified with a fluorophore at the 5'-end and a quencher at the 3'-end to generate molecular beacons, which hybridize with single-stranded DNA to be cleaved by CpRNase HII, the method is suitable for large-scale genotyping, overview
-
-
-
additional information
?
-
-
selective substrate recognition by RNase H1
-
-
-
additional information
?
-
-
substrate specificity and involved active site residues of RNases HII and HIII, overview
-
-
-
additional information
?
-
-
substrate specificity of RNase H1 with modifies heteroduplexes, overview
-
-
-
additional information
?
-
-
member of the nucleotidyl-transferase superfamily and endo-nucleolytically cleaves the RNA portion in RNA/DNA hybrids and removes RNA primers from Okazaki fragments. Enzyme binds RNA and DNA duplexes but is unable to cleave either
-
-
-
additional information
?
-
-
both modification by unlocked nucleic acids and 4'-C-hydroxymethyl-DNA gap insertions are compatible with RNase H activity when used sparingly. Multiple 4'-C-hydroxymethyl-DNA modifications are better tolerated by RNase H than multiple unlocked nucleic acid modifications in the gap
-
-
-
additional information
?
-
Q9X122
ribonuclease H is an enzyme that specifically cleaves RNA of RNA?DNA hybrids
-
-
-
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids
-
-
-
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
-
-
-
additional information
?
-
-
RNase H specifically hydrolyzes the RNA strand of RNA/DNA hybrids in the presence of divalent metal ions, such as Mg2+ and Mn2+
-
-
-
additional information
?
-
Q9X017
RNase H2 hydrolyzes RNA of RNA/DNA hybrids and can nick duplex DNAs containing a single ribonucleotide. It shows a unique mechanism of recognition and substrate-assisted cleavage with preference for junction substrates. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion
-
-
-
additional information
?
-
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
-
-
-
additional information
?
-
-
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
-
additional information
?
-
Q9CWY8
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
-
additional information
?
-
Q9X122
determination of cleavage-site specificity, overview
-
-
-
additional information
?
-
-
model for the complex between Bst-RNase H3 and RNA/DNA hybrid and substrate binding mechanism, overview
-
-
-
additional information
?
-
-
substrate is [alpha-32P]ATP-labeled poly(rA)/poly(dT)
-
-
-
additional information
?
-
-
the DNA/RNA duplex SP hybrid is a substrate for the enzyme while the RP hybrid is not. Structure-activity relationship, and NMR analysis of structural features important for enzyme activity, overview. A fully RP BH3 DNA/RNA hybrid might not be a substrate for RNase H1, NMR structure. Structural analysis of stereoregular borano phosphate modifications
-
-
-
additional information
?
-
-
the enzyme utilizes hybrid RNA/DNA as a substrate. Cleavage activity of RNase HII with different oligomeric substrates, overview
-
-
-
additional information
?
-
-
the enzyme can cleave a DNA-rN1-DNA/DNA substrate (rN1, one ribonucleotide) in vitro, e.g. a RNA-DNA hybrid consisting of CGTCCCaCCGTGC and aucagaaaaAGAGCG strands (capital letters and small bold letters represent DNA and RNA, respectively)
-
-
-
additional information
?
-
Daucus carota GD-2
-
no degradation of single stranded RNA
-
-
-
additional information
?
-
Q25C12
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
-
additional information
?
-
Chlamydia pneumoniae AR39
-
the enzyme can cleave a DNA-rN1-DNA/DNA substrate (rN1, one ribonucleotide) in vitro, e.g. a RNA-DNA hybrid consisting of CGTCCCaCCGTGC and aucagaaaaAGAGCG strands (capital letters and small bold letters represent DNA and RNA, respectively)
-
-
-
additional information
?
-
Chlamydia pneumoniae AR39
-
substrate specificity and involved active site residues of RNases HII and HIII, overview
-
-
-
additional information
?
-
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Thermotoga maritima DSM 3109
Q9X017
-
-
-
?
DNA-RNA duplex + H2O
?
show the reaction diagram
-
specific cleavage of the RNA part
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
Q6L6Q4
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
show the reaction diagram
-
strategy for regulating RNA digestion by RNase H by using a light-activated DNA hairpin, overview
-
-
?
DNA-RNA hybrid + H2O
ssDNA + 5'-phosphomonoester oligonucleotides
show the reaction diagram
-
in the pause of minus strang synthesis, RNAse H degrades the RNA template, with the exception of the polypurine tract sequence, immediately upstream of U3, which serves as a primer for plus-strand synthesis
-
-
?
RNA*DNA hybrid + H2O
?
show the reaction diagram
-
cleaves the RNA portion
-
-
?
RNA-DNA heteroduplex + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
RNase H2 incises the DNA 5'-of the ribonucleotide, generating DNA containing 3'-hydroxyl and 5'-phosphoribonucleotide ends
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
-
the enzyme may play a role in ribonucleotide excision from genomic DNA during replication
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
-
the enzyme could be involved in the removal of RNA primers during DNA replication
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
E8T217
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
P03355
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
A1Z651
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Q9HSF6
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
E0X765
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
O67644
the enzyme specifically cleaves the RNA strand of RNA/DNA hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Saccharomyces cerevisiae W-303
-
-
-
-
?
RNA-DNA hybrid + H2O
?
show the reaction diagram
Thermovibrio ammonificans DSM 15698
E8T217
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Chlamydia pneumoniae AR39
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
Halobacterium salinarum NRC-1
Q9HSF6
-
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
show the reaction diagram
-
enzyme removes RNA primers from lagging strand fragments during DNA replication, 5'-to 3'-exonuclease activity, degradation of the RNA portion of the duplex
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
show the reaction diagram
O29634
RNA primer recognition and removal during DNA replication
-
-
?
RNA-DNA/DNA hybrid + H2O
?
show the reaction diagram
-
PabRNase HII acts as a specific endonuclease on RNA-DNA/DNA duplexes. Specific cleavage, one nucleotide upstream of the RNA-DNA junction, occurs on a substrate in which RNA initiators is fully annealed to the cDNA template. Additionally, PabRNase HII cleaves a single ribonucleotide embedded in a double-stranded DNA
-
-
?
ssDNA-dsDNA + H2O
?
show the reaction diagram
-
5'-to 3'-exonuclease activity, exonuclease activity removing short oligonucleotides of 3-30 nucleotides from adjacent DNA
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
show the reaction diagram
-
-
-
?
additional information
?
-
-
presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
-
-
-
additional information
?
-
-
the enzyme is regulated by a unique redox switch formed by adjacent Cys147 and Cys148
-
-
-
additional information
?
-
Q8WR57
the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
-
-
-
additional information
?
-
Q8WSZ0
the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
-
-
-
additional information
?
-
-
member of the nucleotidyl-transferase superfamily and endo-nucleolytically cleaves the RNA portion in RNA/DNA hybrids and removes RNA primers from Okazaki fragments. Enzyme binds RNA and DNA duplexes but is unable to cleave either
-
-
-
additional information
?
-
Q9X122
ribonuclease H is an enzyme that specifically cleaves RNA of RNA?DNA hybrids
-
-
-
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids
-
-
-
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
-
-
-
additional information
?
-
-
RNase H specifically hydrolyzes the RNA strand of RNA/DNA hybrids in the presence of divalent metal ions, such as Mg2+ and Mn2+
-
-
-
additional information
?
-
Q9X017
RNase H2 hydrolyzes RNA of RNA/DNA hybrids and can nick duplex DNAs containing a single ribonucleotide. It shows a unique mechanism of recognition and substrate-assisted cleavage with preference for junction substrates. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion
-
-
-
additional information
?
-
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
-
-
-
additional information
?
-
-
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
-
additional information
?
-
Q9CWY8
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
-
additional information
?
-
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
-
binding structure
Ca2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Co2+
-
divalent metal required, optimal concentration: 20 mM, 70% of the activity with Mg2+
Co2+
-
activates cleavage of only poly(A) hybrids
Co2+
-
with Co2+ as activator the decreasing order of preference is G, A, U, C
Co2+
-
cobalt hexaamine activates
Co2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Co2+
P10442
activates
Co2+
Q25C12
activates, best at 0.5 mM
Co2+
-
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions. The enzyme cleaves an RNA/RNA duplex in the presence of Mn2+ or Co2+
Co2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimum concentration of Co2+ or Ni2+ needed for aRNase HII activity is 1 mM. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Co2+
Q9YET5
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Co2+
-
10 mM Co2+ supports activity, with only minor inhibition observed at higher concentrations
Co3+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Cu2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
K+
-
required
K+
O67644
the enzyme exhibits the highest activity in the presence of 100 mm KCl
K+
-
optimum KCl concentration of 100-150 mM
KCl
-
stimulates enzyme HB2
KCl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. KCl is more efficient than NaCl
KCl
-
activity increases with concentrations up to 50 mM
KCl
-
activates at 50 mM, inhibits at 200 mM
KCl
Q6L6Q4
highly activating, best at 100-200 mM salt, KCl is preferred
KCl
P10442
equally activating as NaCl
KCl
Q25C12
activates best at 110 mM, preferred to NaCl
KCl
Q9X122
activates, best at 50 mM for the full-length enzyme, and at 10 mM for the C-terminal domain
Mg2+
-
absolute requirement for divalent cations, preferably Mg2+, optimal activity at 25 mM
Mg2+
-
Mg2+ activates more than Mn2+, RNase H(70); Mn2+ activates more than Mg2+, RNase H(42)
Mg2+
-
divalent cation required; Mn2+ is preferred over Mg2+
Mg2+
-
divalent cation required; optimal concentration: 2 mM
Mg2+
-
activates cleavage of only the hybrid combinations containing purine ribo strands
Mg2+
-
with Mg2+ as activator the decreasing order of preference is A, U/C, G
Mg2+
-
optimal activity at 10 mM
Mg2+
-
required, optimal activity at 2-4 mM
Mg2+
-
absolute requirement for Mg2+, optimal activity at 2-6 mM MgCl2
Mg2+
-
divalent cation required; Mg2+ is preferred over Mn2+; optimal concentration is 6 mM
Mg2+
-
required, optimal concentration: 17 mM
Mg2+
-
required, optimal concentration: 10-15 mM Mg2+
Mg2+
-
isoenzyme I and II both require 10-15 mM Mg2+ for maximal activity. Isoenzyme II is maximally activated by Mg2+, some activity with Mn2+
Mg2+
-
Mg2+-dependent enzyme requires 15-20 mM Mg2+ for maximal activity; optimal activity with 10-15 mM
Mg2+
-
Mg2+-dependent enzyme requires 10-15 mM Mg2+ for optimal activity
Mg2+
-
optimal concentrations for the 4 enzyme forms at pH 7.6 and at pH 8.3
Mg2+
-
Mn2+ or Mg2+ required
Mg2+
-
enzyme form H2: requirement for divalent metal ion can be satisfied only by Mg2+. Enzyme form H1: requirement for a divalent metal ion can be satisfied by Mg2+ or with a stronger preference with Mn2+
Mg2+
-
required
Mg2+
-
characterization of the strong magnesium-binding site
Mg2+
-
broad optimum around 20 mM; required
Mg2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Mg2+
-
enzyme is stimulated equally well by Mg2+, optimum concentration 5-10 mM, or Mn2+, optimum concentration 0.5-0.6 mM
Mg2+
-
required
Mg2+
-
ribonuclease H IIa activity is preferentially activated by Mn2+ as opposed to Mg2+
Mg2+
-
dependent on, can substitute for Mg2+, activates the full length enzyme dependent on the N-terminal 47 amino acids
Mg2+
P0A7Y4
maximal activity at 5 mM, binds to metal ion binding site 1 not 2, required, can substitute for Mn2+
Mg2+
-
1:1 binding stoichiometry in absence of substrate at pH 8.0, activates, no binding to the enzyme but still weak activation without substrate at pH 6.5
Mg2+
-
required
Mg2+
-
absolutely dependent on for activity, can be substituted by Mn2+
Mg2+
O29634
dependent on
Mg2+
-
binding involves Asp10 and is pH-dependent, binds in the active site pocket of the natively folded enzyme only, stabilizes the enzyme conformation, effect of metal binding on enzyme folding kinetics
Mg2+
Q6L6Q4
required, highest activity at 50 mM
Mg2+
-
binding structure
Mg2+
Q25C12
activates, best at 5 mM
Mg2+
-
a divalent metal ion is required, dependent on the isozyme
Mg2+
-
required, best at 50 mM; the enzyme requires Mn2+ or Mg2+ ions, Mg2+ is preferred, coordinated with Asp97, Glu98, and Asp202
Mg2+
-
activates
Mg2+
-
required
Mg2+
-
the inability of the enzyme to cleave DNA is due to the deviating curvature of the DNA strand relative to the substrate RNA strand and the absence of Mg2+ at the active site
Mg2+
-
the two Mg2+ support the formation of a meta-stable phosphorane intermediate along the reaction
Mg2+
Q5TBB1, Q8TDP1
highest activity in presence of 5-10 mM; highest activity in presence of 5-10 mM; highest activity in presence of 5-10 mM
Mg2+
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
Mg2+
-
activates
Mg2+
Q9X122
dependent on
Mg2+
-
activates, required
Mg2+
-
the type 2 RNase H is an Mg2+ and alkaline pH-dependent enzyme
Mg2+
-
required, best at 10 mM
Mg2+
-
required
Mg2+
-
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview
Mg2+
-
two Mg2+ ions in the RNase H active site, required. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
Mg2+
-
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions
Mg2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimal enzyme activities in the presence of Mg2+ or Mn2+ are 3fold to 7fold higher than that with the other two metals. Maximum aRNase HII activity is observed at concentrations of 6.4 mM Mg2+. The specific activity determined in the presence of 50 mM Mn2+ is 35% of that determined in the presence of 6.4 mM Mg2+. When Mn2+ is added in the presence of 1.6 mM Mg2+, the enzyme activity increases gradually as the Mn2+ concentration reaches 50 mM and decreases after that point. At equal concentrations of Mn2+ and Mg2+ (1.6 mM), the enzyme activity is reduced 10-fold compared to the activity in the presence of only Mg2+. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Mg2+
Q9YET5
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Mg2+
O67644
highest activity in the presence of 10 mM MgCl2
Mg2+
-
Mg2+ best supports the enzyme, with an optimal concentration of 10 mM
Mg2+
-
the optimum concentration is 10 mM
Mg2+
-
the optimum concentration is 1 mM
Mg2+
E0X765
the enzyme prefers Mg2+ to Mn2+ ions for activity with maximal activity at 10 mM MgCl2
Mg2+
-
native cofactor
Mg2+
P03355
native cofactor
Mg2+
-
required
Mg2+
-
the enzyme is stabilized in the presence of Mg2+
Mn2+
-
cation requirement can be fullfilled to some extent by 2 mM Mn2+
Mn2+
-
Mg2+ activates more than Mn2+, RNase H(70); Mn2+ activates more than Mg2+, RNase H(42)
Mn2+
-
divalent cation required; Mn2+ is preferred over Mg2+
Mn2+
-
divalent cation required; optimal concentration: 25 mM, 40% of the activation with Mg2+
Mn2+
-
activates enzymatic cleavage of all hybrid combinations
Mn2+
-
with Mg2+ as activator the decreasing order of preference is A, U, C, G
Mn2+
-
optimal activity at 1 mM
Mn2+
-
divalent cation required; Mn2+ is preferred over Mg2+
Mn2+
-
divalent cation required; Mg2+ is preferred over Mn2+; optimal concentration is 2 mM
Mn2+
-
optimal concentration 0.6 mM
Mn2+
-
isoenzyme II is maximally active at 0.4 mM, some activity with Mg2+
Mn2+
-
0.4 mM Mn2+ required for optimal activity, some activity with Mg2+
Mn2+
-
0.4 mM Mn2+ required for optimal activity, some activity with Mg2+
Mn2+
-
optimal concentrations for the 4 enzyme forms at pH 7.6 and at pH 8.3
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
Mn2+ or Mg2+ required; optimal concentration: 1.2 mM
Mn2+
-
enzyme form H1: requirement for a divalent metal ion can be satisfied by Mg2+ or with a stronger preference with Mn2+
Mn2+
-
slightly active with Mn2+
Mn2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Mn2+
-
enzyme is stimulated equally well by Mg2+, optimum concentration 5-10 mM, or Mn2+, optimum concentration 0.5-0.6 mM
Mn2+
-
ribonuclease H IIa activity is preferentially activated by Mn2+ as opposed to Mg2+
Mn2+
-
can substitute for Mg2+, activates N-terminally truncated mutant RNHIDELTA47 and inhibits the full length enzyme dependent on the presence of the N-terminal 47 amino acids
Mn2+
P0A7Y4
required, maximal activity at 0.002-0.005 mM, can substitute for Mg2+, activates up to 0.1 mM, inhibitory above, enzyme contains 2 metal ion binding sites 1 and 2 with regulatory influence on each other, activating metal ion binding site is site 1, inhibitory binding site is site 2, overview, mutants E48A, E48Q, D134A, and D134N have only 1 active Mn2+-binding site
Mn2+
-
1:1 binding stoichiometry in absence of substrate at pH 8.0, best activator, maximal activity at 10 mM and pH 8.0
Mn2+
-
absolutely dependent on for activity, can be substituted by Mg2+
Mn2+
-
-
Mn2+
-
binding structure
Mn2+
P10442
activates
Mn2+
Q25C12
activates, best at 1 mM, strongly preferred divalent cation
Mn2+
-
a divalent metal ion is required, dependent on the isozyme
Mn2+
-
activates, two single binding sites: site 1 is formed by Glu48, Asp10, and Asp70, site 2 is formed by Asp10 and Asp134, Glu48 and Asp134 are absolutely required for enzyme activation, binding structure and one-to-two metal mechanism, overview
Mn2+
-
less active than Mg2+, best at 10 mM; the enzyme requires Mn2+ or Mg2+ ions, Mg2+ is preferred, coordinated with Asp97, Glu98, and Asp202
Mn2+
Q8U036
wild-type digests RNA-RNA duplexes in presence of Mn2+
Mn2+
Q5TBB1, Q8TDP1
0.1-1 mM, 20-30% of maximum activity; 0.1-1 mM, 20-30% of maximum activity; 0.1-1 mM, 20-30% of maximum activity
Mn2+
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
Mn2+
-
the activity of wild-type protein is stimulated by Mn2+, whereas this cation significantly inhibits the activity of C-terminal truncated mutant proteins
Mn2+
Q9X122
activates, less active than Mg2+
Mn2+
-
activates, required
Mn2+
-
required, best at 1 mM
Mn2+
-
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview
Mn2+
-
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions. The enzyme cleaves an RNA/RNA duplex in the presence of Mn2+ or Co2+
Mn2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimal enzyme activities in the presence of Mg2+ or Mn2+ are 3fold to 7fold higher than that with the other two metals. Maximum aRNase HII activity is observed at concentrations of 50 mM Mn2+. The specific activity determined in the presence of 50 mM Mn2+ is 35% of that determined in the presence of 6.4 mM Mg2+. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Mn2+
Q9YET5
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Mn2+
A1Z651
optimal RNase H activity in the presence of Mn2+ and not Mg2+
Mn2+
-
required
Mn2+
O67644
highest activity in the presence of 5 mM MnCl2
Mn2+
-
5 mM Mn2+ supports activity, with only minor inhibition observed at higher concentrations
Mn2+
-
the optimum concentration is 10 mM
Mn2+
-
the optimum concentration is 1 mM
Na+
O67644
the enzyme exhibits the highest activity in the presence of 100 mm NaCl
NaCl
-
stimulates
NaCl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. KCl or NH4Cl is more efficient than NaCl
NaCl
-
activates at 50 mM, inhibits at 200 mM
NaCl
Q6L6Q4
activating, best at 100-200 mM salt
NaCl
P10442
equally activating as KCl
NaCl
Q25C12
activates best at 60 mM
NH4Cl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. NH4Cl is more efficient than NaCl
Ni2+
-
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions
Ni2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimum concentration of Co2+ or Ni2+ needed for aRNase HII activity is 1 mM. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Ni2+
-
exhibits only modest activity as cofactor
Zn2+
O29634
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Zn2+
-
exhibits only modest activity as cofactor
Mn2+
E0X765
the enzyme prefers Mg2+ to Mn2+ ions for activity with maximal activity at 0.1 mM MnCl2
additional information
-
the enzyme exists in two different conformations depending on the type of divalent cation activation
additional information
P0A7Y4
metal ion binding sites are located in the active site
additional information
-
enzyme is divalent metal ion-dependent, one metal ion binding mechanism, pH-dependence, kinetics, and thermodynamics for Mg2+, Mn2+, wild-type and mutant enzymes, substrate is involved in metal ion positioning and binding, Ca2+ and Ba2+ cannot substitute for Mn2+ or Mg2+
additional information
-
no activity in absence of Mg2+ or Mn2+, and in presence of 10 mM of Ba2+, Ca2+, Co2+, Zn2+, Cu2+, Fe2+, or Sr2+
additional information
-
enzyme requires divalent cations
additional information
O29634
metal coordination in the active site
additional information
-
type 2 enzyme requires divalent cations
additional information
Q6L6Q4
Mg2+ cannot be substituted by Co2+ and Ni2+, and only partially by Mn2+
additional information
-
the enzyme performs a two-metal catalysis, with metal A activating the nucleophile and metal B stabilizing the transition state, mechanism and structures, overview
additional information
P10442
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
Q25C12
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
Q9X122
Tma-RNase HI prefers Mg2+ to Mn2+ for activity, and specifically loses most of the Mg2+-dependent activity on removal of the hybrid binding domain and 87% of it by the mutation at the hybrid binding domain. Activity profiles of different metals and salt concentrations
additional information
O67644
the enzyme exhibits little activity (less than 0.002% of the maximal activity) in the presence of ZnCl2, CaCl2, CoCl2 and NiCl2
additional information
-
not stimulated by Ca2+
additional information
Q9HSF6
the enzyme requires either salt or divalent metal ions for folding. The enzyme exhibits activity in the presence of divalent metal ions regardless of the presence or absence of 3 M NaCl. However, higher concentrations of divalent metal ions are required for activity in the absence of salt to facilitate folding
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(1R,3R,4R,5R,8S)-8-benzyloxy-1-benzyloxymethyl-5-benzyloxyamino-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5R,8S)-8-benzyloxy-1-benzyloxymethyl-5-trifluoroacetamino-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-((methylthio)thiocarbonyl)oxy-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-(4-methylbenzoyl)-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-hydroxy-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane (20a) and (1R,3R,4R,5R,8S)-8-benzyloxy-1-benzyloxymethyl-5-hydroxy-3-(thymin-1-yl)-2-oxabicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-methoxalyloxy-5-methyl-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,8S)-8-benzyloxy-1-benzyloxymethyl-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,8S)-8-benzyloxy-1-benzyloxymethyl-5-one-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(NH4)2SO4
-
above 0.1 M
(NH4)2SO4
-
isoenzyme II, 80% inhibition at 200 mM
(NH4)2SO4
-
200 mM, 80% inhibition of Mn2+-dependent enzyme
(NH4)2SO4
-
above 60 mM
(NH4)2SO4
-
complete inhibition at 100 mM, in presence of 10 mM MgCl2
(NH4)2SO4
-
moderate
1,10-phenanthroline
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
1-(2-O-acetyl-3,5-O-benzyl-4-C-cyanoethyl-beta-D-ribofuranosyl)-thymine
-
-
1-(3,5-O-benzyl-2-O-phenoxythiocarbonyl-4-C-propionaldehyde-beta-D-ribofuranosyl)thymineO-benzyloxime
-
-
1-(3,5-O-benzyl-4-C-cyanoethyl-2-O-hydroxyl-beta-D-ribofuranosyl)-thymine
-
-
1-(3,5-O-benzyl-4-C-propionaldehyde-2-O-hydroxyl-beta-D-ribofuranosyl)thymine O-benzyl oxime
-
-
2-(2,3-dimethylphenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
-
2-(2,5-dimethylphenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
-
2-(4,6-dimethyl-3-oxo-1,2-benzothiazol-2(3H)-yl)-N-propylacetamide
-
-
2-(4-chlorophenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
-
2-(6-fluoro-3-oxo-1,2-benzothiazol-2(3H)-yl)-N-(4-methylphenyl)acetamide
-
-
2-phenyl-1,2-benzothiazol-3(2H)-one
-
-
2-[(cyclopentylcarbonyl)amino]-4-ethyl-5-methylthiophene-3-carboxamide
-
-
3,5-di-O-benzyl-4-C-cyanoethyl-1,2-O-isopropylidene-alpha-D-ribofuranose
-
-
4-[(4'-aminomethyl-1,1'-biphenyl)methyl]-1-hydroxy-1,8-naphthyridin-2-one
A1Z651
-
-
5-nitrofuran-2-carboxylic acid [[4-(4-bromophenyl)-thiazol-2-yl]-(tetrahydrofuran-2-ylmethyl)-carbamoyl]-methyl ester
-
derivative of 5-nitrofuran-2-carboxylic acid carbamoyl methyl ester. 20-25 microM effectively inhibit HIV-1 replication
6-(naphthalen-2-yl)-3-(pyridin-3-yl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole
-
-
6-fluoro-2-(2-methylphenyl)-1,2-benzothiazol-3(2H)-one
-
-
6-fluoro-2-(4-methylphenyl)-1,2-benzothiazol-3(2H)-one
-
-
7-(furan-2-yl)-2-hydroxy-isoquinoline-1,3(2H,4H)-dione
A1Z651
YLC2-155
-
acetonitrile
-
20%, 50% loss of activity
alpha-thujaplicin
-
i.e. 2-hydroxy-3-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
alpha-thujaplicin
-
i.e. 2-hydroxy-3-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
antisense oligodeoxynucleotides
-
directed against RNA polymerase II, replication protein A, and Ha-ras, determination of response in expression levels of the enzyme type 1 and 2, overview
-
beta-thujaplicin
-
i.e. 2-hydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
beta-thujaplicin
-
i.e. 2-hydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
beta-thujaplicinol
-
i.e. 2,7-dihydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
Ca2+
-
Ca2+ substitution of either of the two active-site Mg2+ ions substantially increases the height of the reaction barrier and thereby abolishes the catalytic activity
Co2+
-
in presence of Mg2+, inhibition
Co2+
Q6L6Q4
over 95% inhibition at 5 mM and below
Cu2+
-
in presence of Mg2+, inhibition
Dextran
-
-
Dextran
-
inhibits degradation of poly(rA)*poly(dT), no inhibition of degradation by phi174DNA-RNA. Dextran does not interfere with the recognition site, but rather blocks hydrolysis
diphosphate
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
DNA
-
single-stranded or double-stranded, very strong
DTT
-
-
EDTA
-
-
Ethidium bromide
-
-
Fe2+
-
in presence of Mg2+, inhibition
gamma-thujaplicin
-
i.e. 2-hydroxy-5-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
gamma-thujaplicin
-
i.e. 2-hydroxy-5-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
Hg2+
-
-
KCl
-
enzyme form HA1, HA2, and HB1
KCl
-
activity of enzyme form H1 decreases rapidly above 50 mM and becomes nearly abolished at 150 mM
KCl
-
half-maximal inhibition at 150 mM
KCl
-
activates by 50% at 50 mM, inhibits by 90% at 200 mM
manicol
-
i.e. 1,2,3,4-tetrahydro-2,7-dihydroxy-9-methyl-2-(1-methylethyl)-6H-benzocyclohepten-6-one
Mg2+
-
Mg2+ is inhibitory at concentrations above 10 mM
Mn2+
-
in presence of Mg2+, strong inhibition
Mn2+
-
can substitute for Mg2+, activates N-terminally truncated mutant RNHIDELTA47 and inhibits the full length enzyme dependent on the presence of the N-terminal 47 amino acids
Mn2+
P0A7Y4
wild-type enzyme, above 0.1 mM, activating below, activating metal ion binding site is site 1, inhibitory binding site is site 2
Mn2+
Q6L6Q4
40% inhibition at 100 mM
Mn2+
-
Mn2+ inhibition of in vitro reverse transcriptase activity is greatly reduced in all the suppressor mutants, whereas RNAse H activity and cleavage specificity remain largely unchanged
N-(5-benzyl-1,3,4-thiadiazol-2-yl)-2-ethylhexanamide
-
-
N-benzyl-2-(6-fluoro-3-oxo-1,2-benzothiazol-2(3H)-yl)acetamide
-
-
N-cyclopentyl-2-(4,6-dimethyl-3-oxo[1,2]thiazolo[5,4-b]pyridin-2(3H)-yl)acetamide
-
-
N-cyclopropyl-1-methyl-3-oxo-1,3-dihydro-2,1-benzothiazole-5-sulfonamide
-
-
N-ethylmaleimide
-
inhibits wild-type enzyme and deletion mutant H1[DELTA1-73]
NaCl
-
activity of enzyme form H1 decreases rapidly above 50 mM and becomes nearly abolished at 150 mM
NaCl
-
activates by 50% at 50 mM, inhibits by 90% at 200 mM
NaF
-
inhibition of Mg2+-dependent enzyme
NEM
-
-
NEM
-
the Mg2+-dependent activity is inhibited by 60% at 20 mM. The Mn2+-dependent activity is unaffected
NEM
-
0.03 mM, 50% inhibition after 30 min
NEM
-
2 mM, 80% inhibition of Mn2+-dependent enzyme, complete inhibition of Mg2+-dependent enzyme
NEM
-
2 mM or above
NEM
-
enzyme form H2. No effect on enzyme form H1
NEM
-
2 mM, 50% inhibition
NEM
-
Mn2+-dependent activity is moderately sensitive, even at high concentrations
NEM
-
Mg2+-dependent activity is highly sensitive
NH4Cl
-
activity of enzyme form H1 decreases rapidly above 50 mM and becomes nearly abolished at 150 mM
Ni2+
Q6L6Q4
nearly complete inhibition at 5 mM and below
nootkatin
-
i.e. 2-hydroxy-5-(3-methyl-2-butenyl)-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
nootkatin
-
i.e. 2-hydroxy-5-(3-methyl-2-butenyl)-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
Nucleic acids
-
enzyme form H1 is more susceptible to inhibition than enzyme form H2
-
PCMB
-
in absence of 2-mercaptoethanol
PCMB
-
in absence of 2-mercaptoethanol, isoenzyme I and III are completely inhibited by 0.2 mM PCMB, Activity of isoenzyme II is inhibited 20%
PCMB
-
2 mM, complete inhibition of Mn2+-dependent enzyme and Mg2+-dependent enzyme
poly(rA)
-
noncompetitive
-
poly(rArU)
-
noncompetitive
-
poly(rCdG)
-
uncompetitive
-
poly(rIdC)
-
competitive
-
Polyribonucleotides
-
slight
reovirus RNA
-
competitive
-
Rifampicin
-
derivatives
Rifampicin
-
and some derivatives
rifampicin AF/013
-
-
S-adenosylhomocysteine
-
-
S-adenosylmethionine
-
-
S-adenosylmethionine
-
at 35C but not at 0C
S-adenosylmethionine
-
2 mM or above
SDS
-
0.002%, 50% loss of activity
spermidine
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
spermine
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
trihydroxy benzoyl biphenyl carboxylate hydrazone
A1Z651
BHMP07
-
trihydroxybenzoyl naphthyl hydrazone
A1Z651
-
-
tropolone
-
i.e. 2-hydroxy-2,4,6-cycloheptatrien-1-one, slight inhibition
tropolone
-
i.e. 2-hydroxy-2,4,6-cycloheptatrien-1-one
Zn2+
-
in presence of Mg2+, inhibition
Mn2+
-
the activity of wild-type protein is stimulated by Mn2+, whereas this cation significantly inhibits the activity of C-terminal truncated mutant proteins
additional information
-
presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
-
additional information
-
selectivity of tropolone derivatives for RNase H, IC50 values, inhibition mechanism, overview
-
additional information
-
chimeric substrates containing 2'-methoxyethyl nucleotides inhibit human RNase H1 activity
-
additional information
-
a 5' RNA flap Okazaki fragment intermediate impairs PabRNase HII endonuclease activity. Introduction of mismatches into the RNA portion near the RNA-DNA junction decreases both the specificity and the efficiency of cleavage by PabRNase HII
-
additional information
-
drug design and synthesis by 2',4'-propylene-bridged thymidine, and five 8'-Me/NH2/OH variants thereof, introduction into 15mer oligodeoxynucleotides, the compounds inhibit the enzyme by formation of stable complexes with RNA, inhibitory effect of the variants, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(NH4)2SO4
-
ribonuclease H I acts optimally at about 30 mM (NH4)2SO4 in the case of Mn2+ activation, in the presence of Mg2+ ions the enzyme acts best if (NH4)2SO4 is omitted
(NH4)2SO4
-
optimal concentration: 25 mM
(NH4)2SO4
-
100 mM, isoenzyme I and II are activated by 50%. Isoenzyme II shows optimal activity at 50 mM, 80% inhibition at 200 mM
(NH4)2SO4
-
30% activation of Mg2+-dependent enzyme
(NH4)2SO4
-
4fold stimulation at an optimal concentration of 18 mM
2-mercaptoethanol
-
stimulates
2-mercaptoethanol
-
enzyme form H2 is inactive in absence of mercaptoethanol. No effect on enzyme form H1
2-mercaptoethanol
-
-
dithiothreitol
-
optimal concentration is 1 mM
Sulfhydryl reagent
-
is required
-
Sulfhydryl reagent
-
required for maximal activity of the Mn2+-dependent enzyme and the Mg2+-dependent enzyme
-
Sulfhydryl reagent
-
-
-
additional information
-
mRNA/antisense oligodeoxynucleotide duplex formation activates RNase H-mediated hydrolysis of mRNA
-
additional information
-
ability of the DNA and 2'-FANA oligomers of mixed-base composition to elicit human RNase H1 degradation of complementary RNA that is either unstructured or as a hairpin, overview
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000361
5'-(6-carboxy-fluorescein)-cggagaugacgg-3'/5'-CCGTCTCTCCG-3'
Q9YET5
pH 9.0, 30C
-
0.000027
D14R1D3:DNA18
Q9CWY8
mutant R291H, pH 8.0, temperature not specified in the publication
-
0.000028
D14R1D3:DNA18
Q9CWY8
wild-type enzyme, pH 8.0, temperature not specified in the publication
-
0.00003
D14R1D3:DNA18
Q9CWY8
mutant K143I, pH 8.0, temperature not specified in the publication
-
0.000122
DNA-(1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
0.000242
DNA-(2'-alkoxy-1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
0.000532
DNA-(aza-ENA-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
0.000236
DNA-(azetidine-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
0.000083
DNA-(oxetane-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
0.000064
DNA-RNA hybrid
-
pH 7.5, 21C
-
0.0011
DNA-RNA-DNA hybrid
-
mutant A12S/K75M and A12S/K75M/A77P, pH 8.0, 30C
-
0.0013
DNA-RNA-DNA hybrid
-
mutant A12S/A77P, pH 8.0, 30C
-
0.0015
DNA-RNA-DNA hybrid
-
mutant A12S, pH 8.0, 30C
-
0.002
DNA-RNA-DNA hybrid
-
mutant K75M/A77P, pH 8.0, 30C
-
0.0033
DNA-RNA-DNA hybrid
-
mutant D134H and A77P, pH 8.0, 30C
-
0.0061
DNA-RNA-DNA hybrid
-
mutant K75M, pH 8.0, 30C
-
0.0078
DNA-RNA-DNA hybrid
-
wild-type enzyme, pH 8.0, 30C
-
0.0014
DNA/RNA hybrid
-
obtained by transcription of calf thymus DNA
-
0.071
M13 DNA-RNA hybrid
Q25C12
pH 8.5, 15C, recombinant enzyme
-
0.075
M13 DNA-RNA hybrid
Q25C12
pH 8.5, 30C, recombinant enzyme
-
0.26
M13 DNA-RNA hybrid
P10442
pH 8.5, 15C or 30C, recombinant enzyme
-
0.0005
M13 DNA/RNA
-
at 37C
-
0.0011
M13 DNA/RNA
-
at 70C
-
0.00039
M13 DNA/RNA hybrid
Q9X122
wild-type enzyme, pH 9.0, 30C, in presence of 50 mM KCl
-
0.00082
M13 DNA/RNA hybrid
-
pH 8.5, 30C, Mg2+, recombinant wild-type enzyme
-
0.0013
M13 DNA/RNA hybrid
-
pH 8.5, 30C, Mg2+, recombinant mutant K50A
-
0.0005
poly(rAdT)
-
lower than 0.0005 mM
-
0.0016
poly(rAdT)
-
-
-
0.0019
poly(rAdT)
-
-
-
0.012
polyA*dT36
-
pH 8.0, 500 mM NaCl, wild-type enzyme
-
0.00009
RNA*DNA hybrid
-
wild-type enzyme, pH 8.0, 30C
-
0.00026
RNA*DNA hybrid
-
pH 8.5, 30C, recombinant soluble non-tagged enzyme
-
0.00054
RNA*DNA hybrid
-
mutant D135A, pH 8.0, 30C
-
0.00097
RNA*DNA hybrid
-
truncated mutant RNase HII-217, pH 8.0, 30C
-
0.00118
RNA*DNA hybrid
-
mutant E8A, pH 8.0, 30C
-
0.0014
RNA*DNA hybrid
-
mutant H132A, pH 8.0, 30C
-
0.00155
RNA*DNA hybrid
-
truncated mutant RNase HII-207, pH 8.0, 30C
-
0.0019
RNA*DNA hybrid
-
truncated mutant RNase HII-213, pH 8.0, 30C
-
0.00837
RNA*DNA hybrid
-
truncated mutant RNase HII-203, pH 8.0, 30C
-
0.00012
RNA-DNA duplex
Q8U036
mutant F114E, 50C, presence of Mn2+; wild-type, 50C, presence of Mg2+; wild-type, 50C, presence of Mn2+
-
0.00014
RNA-DNA duplex
Q8U036
mutant A115E, 50C, presence of Mn2+
-
0.0002
RNA-DNA duplex
Q8U036
mutant R113E, 50C, presence of Mn2+
-
0.000097
RNA-DNA heteroduplex
-
wild type enzyme, at pH 7.5 and 30C
-
0.000106
RNA-DNA heteroduplex
-
mutant enzyme H264A, at pH 7.5 and 30C
-
0.0011
RNA-DNA hybrid
O67644
wild type enzyme, in 10 mM Tris/HCl (pH 9.0) containing 10 mM MgCl2, 100 mM KCl, 1 mM beta-mercaptoethanol and 0.05 mg/ml bovine serum albumin, at 30C
-
0.0012
RNA-DNA hybrid
O67644
wild type enzyme, in 10 mM Tris/HCl (pH 9.0) containing 10 mM MnCl2, 100 mM KCl, 1 mM beta-mercaptoethanol and 0.05 mg/ml bovine serum albumin, at 30C
-
0.0026
RNA-DNA hybrid
O67644
mutant enzyme Y45A, in 10 mM Tris/HCl (pH 9.0) containing 2 mM MnCl2, 100 mM KCl, 1 mM beta-mercaptoethanol and 0.05 mg/ml bovine serum albumin, at 30C
-
0.0028
RNA-DNA hybrid
O67644
mutant enzyme Y45A, in 10 mM Tris/HCl (pH 9.0) containing 10 mM MgCl2, 100 mM KCl, 1 mM beta-mercaptoethanol and 0.05 mg/ml bovine serum albumin, at 30C
-
0.00006
RNA-DNA*DNA hybrid
O29634
recombinant wild-type enzyme, pH 8.0, 30C
-
0.0016
RNA-DNA*DNA hybrid
O29634
recombinant mutant R146A, pH 8.0, 30C
-
0.00188
RNA-DNA*DNA hybrid
O29634
recombinant mutant K143A, pH 8.0, 30C
-
0.00268
RNA-DNA*DNA hybrid
O29634
recombinant mutant Y164A, pH 8.0, 30C
-
0.0036
RNA-DNA*DNA hybrid
O29634
recombinant mutant R46A, pH 8.0, 30C
-
0.0005
RNA-DNA/DNA hybrid
-
pH 8.0, 37C, purified recombinant His-tagged enzyme
-
0.0013
RNA-RNA duplex
Q8U036
wild-type, 50C, presence of Mn2+
-
0.000143
RNA18:DNA18
Q9CWY8
wild-type enzyme, pH 8.0, temperature not specified in the publication
-
0.000144
RNA18:DNA18
Q9CWY8
mutant R291H, pH 8.0, temperature not specified in the publication
-
0.000158
RNA18:DNA18
Q9CWY8
mutant K143I, pH 8.0, temperature not specified in the publication
-
0.0014
M13 DNA/RNA hybrid
-
pH 8.5, 30C, Mg2+, recombinant mutant V42A
-
additional information
additional information
-
-
-
additional information
additional information
-
-
-
additional information
additional information
-
thermodynamics of wild-type and mutant enzymes
-
additional information
additional information
-
Km at 50 mM NaCl not measurable
-
additional information
additional information
-
folding kinetics of the enzyme with Mg2+ bound or metal-free
-
additional information
additional information
-
determination of enzyme surface enzyme kinetics by surface plasmon resonance imaging and surface plasmon fluorescence spectroscopy, kinetic analysis, overview
-
additional information
additional information
-
kinetics of isozymes
-
additional information
additional information
-
thermodynamics, heat capacity measurement, thermal stability and flexibility of the enzyme
-
additional information
additional information
-
thermodynamics, overview
-
additional information
additional information
-
binding affinity of the chimeric antisense oligonucleotides to the target RNA and DNA, Michaelis-Menten kinetics, overview, dependence of the initial velocity on the substrate concentration, overview
-
additional information
additional information
-
Michaelis-Menten kinetics with different DNA-RNA hybrids
-
additional information
additional information
-
multiple-turnover kinetics with heteroduplexes
-
additional information
additional information
-
thermodynamic analyses of chimeric proteins, overview
-
additional information
additional information
-
thermodynamic analyses of mutant enzymes, overview
-
additional information
additional information
-
kinetics of recombinant wild-type and mutant enzymes, overview
-
additional information
additional information
Q9CWY8
substrate hydrolysis by RNase H2 follows Michaelis-Menten kinetics
-
additional information
additional information
O29912
kinetic parameters for the enzyme in the absence and presence of proliferating cell nuclear antigen (PCNA)
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.158
D14R1D3:DNA18
Q9CWY8
mutant R291H, pH 8.0, temperature not specified in the publication
-
0.35
D14R1D3:DNA18
Q9CWY8
mutant K143I, pH 8.0, temperature not specified in the publication
-
0.4
D14R1D3:DNA18
Q9CWY8
wild-type enzyme, pH 8.0, temperature not specified in the publication
-
2.43
DNA-(1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
2.5
DNA-(2'-alkoxy-1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
3.97
DNA-(aza-ENA-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
2.13
DNA-(azetidine-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
1.47
DNA-(oxetane-T)-antisense-RNA hybrid
-
pH 7.5, 21C
-
1.54
DNA-RNA hybrid
-
pH 7.5, 21C
-
0.95
DNA-RNA hydrid
-
pH 7.8-7.9, 25C
-
0.003
DNA-RNA-DNA hybrid
-
mutant D134H, pH 8.0, 30C
-
0.075
DNA-RNA-DNA hybrid
-
mutant A12S, pH 8.0, 30C
-
0.082
DNA-RNA-DNA hybrid
-
wild-type enzyme, pH 8.0, 30C
-
0.122
DNA-RNA-DNA hybrid
-
mutant A77P, pH 8.0, 30C
-
0.133
DNA-RNA-DNA hybrid
-
mutant K75M, pH 8.0, 30C
-
0.2
DNA-RNA-DNA hybrid
-
mutant A12S/K75M, pH 8.0, 30C
-
0.25
DNA-RNA-DNA hybrid
-
mutant A12S/A77P, pH 8.0, 30C
-
0.33
DNA-RNA-DNA hybrid
-
mutant K75M/A77P, pH 8.0, 30C
-
0.11
polyA*dT36
-
pH 8.0, 500 mM NaCl, wild-type enzyme
-
0.64
polyA*dT36
-
pH 8.0, 50 mM NaCl, wild-type enzyme
-
0.0068
RNA-DNA duplex
Q8U036
mutant F114E, 50C, presence of Mn2+
-
0.11
RNA-DNA duplex
Q8U036
mutant R113E, 50C, presence of Mn2+
-
0.188
RNA-DNA duplex
Q8U036
wild-type, 50C, presence of Mn2+
-
0.255
RNA-DNA duplex
Q8U036
mutant A115E, 50C, presence of Mn2+
-
0.283
RNA-DNA duplex
Q8U036
wild-type, 50C, presence of Mg2+
-
0.025
RNA-DNA heteroduplex
-
mutant enzyme H264A, at pH 7.5 and 30C
-
3.5
RNA-DNA heteroduplex
-
wild type enzyme, at pH 7.5 and 30C
-
0.133
RNA-DNA*DNA hybrid
O29634
recombinant wild-type enzyme, pH 8.0, 30C
-
0.192
RNA-DNA*DNA hybrid
O29634
recombinant mutant R146A, pH 8.0, 30C
-
0.2
RNA-DNA*DNA hybrid
O29634
recombinant mutant R46A and K143A, pH 8.0, 30C
-
0.208
RNA-DNA*DNA hybrid
O29634
recombinant mutant Y164A, pH 8.0, 30C
-
0.093
RNA-DNA/DNA hybrid
-
pH 8.0, 37C, purified recombinant His-tagged enzyme
-
0.0005
RNA-RNA duplex
Q8U036
wild-type, 50C, presence of Mn2+
-
0.983
RNA18:DNA18
Q9CWY8
mutant R291H, pH 8.0, temperature not specified in the publication
-
2.1
RNA18:DNA18
Q9CWY8
mutant K143I, pH 8.0, temperature not specified in the publication
-
3.48
RNA18:DNA18
Q9CWY8
wild-type enzyme, pH 8.0, temperature not specified in the publication
-
0.45
DNA-RNA-DNA hybrid
-
mutant A12S/K75M/A77P, pH 8.0, 30C
-
additional information
additional information
-
-
-
additional information
additional information
-
-
-
additional information
additional information
-
the logarithm of the turnover number of the enzyme increases steeply with pH until a pH-independent region is reached close to neutrality
-
additional information
additional information
O29912
kinetic parameters for the enzyme in the absence and presence of proliferating cell nuclear antigen (PCNA)
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5
D14R1D3:DNA18
Q9CWY8
mutant R291H, pH 8.0, temperature not specified in the publication
0
11.67
D14R1D3:DNA18
Q9CWY8
mutant K143I, pH 8.0, temperature not specified in the publication
0
240
RNA-DNA heteroduplex
-
mutant enzyme H264A, at pH 7.5 and 30C
0
36000
RNA-DNA heteroduplex
-
wild type enzyme, at pH 7.5 and 30C
0
185.7
RNA-DNA/DNA hybrid
-
pH 8.0, 37C, purified recombinant His-tagged enzyme
0
6.67
RNA18:DNA18
Q9CWY8
mutant R291H, pH 8.0, temperature not specified in the publication
0
13.33
RNA18:DNA18
Q9CWY8
mutant K143I, pH 8.0, temperature not specified in the publication
0
25
RNA18:DNA18
Q9CWY8
wild-type enzyme, pH 8.0, temperature not specified in the publication
0
15
D14R1D3:DNA18
Q9CWY8
wild-type enzyme, pH 8.0, temperature not specified in the publication
0
additional information
additional information
O29912
kinetic parameters for the enzyme in the absence and presence of proliferating cell nuclear antigen (PCNA)
0
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00019
2-(2,3-dimethylphenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00045
2-(2,5-dimethylphenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00833
2-(4,6-dimethyl-3-oxo-1,2-benzothiazol-2(3H)-yl)-N-propylacetamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.0005
2-(4-chlorophenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00005
2-(6-fluoro-3-oxo-1,2-benzothiazol-2(3H)-yl)-N-(4-methylphenyl)acetamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00002
2-phenyl-1,2-benzothiazol-3(2H)-one
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.0019
2-[(cyclopentylcarbonyl)amino]-4-ethyl-5-methylthiophene-3-carboxamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.000357
4-[(4'-aminomethyl-1,1'-biphenyl)methyl]-1-hydroxy-1,8-naphthyridin-2-one
A1Z651
with RNA-DNA hybrid HTS-1 as substrate, at pH 7.8 and 37C
-
0.000402
4-[(4'-aminomethyl-1,1'-biphenyl)methyl]-1-hydroxy-1,8-naphthyridin-2-one
A1Z651
with RNA-DNA hybrid HTS-2 as substrate, at pH 7.8 and 37C
-
0.05
5-nitrofuran-2-carboxylic acid [[4-(4-bromophenyl)-thiazol-2-yl]-(tetrahydrofuran-2-ylmethyl)-carbamoyl] methyl ester
-
inhibitory activity against human RNase H1. IC50 value about 50 microM
0.0064
6-(naphthalen-2-yl)-3-(pyridin-3-yl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00001
6-fluoro-2-(2-methylphenyl)-1,2-benzothiazol-3(2H)-one
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.0002
6-fluoro-2-(4-methylphenyl)-1,2-benzothiazol-3(2H)-one
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.0054
N-(5-benzyl-1,3,4-thiadiazol-2-yl)-2-ethylhexanamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00048
N-benzyl-2-(6-fluoro-3-oxo-1,2-benzothiazol-2(3H)-yl)acetamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.00332
N-cyclopentyl-2-(4,6-dimethyl-3-oxo[1,2]thiazolo[5,4-b]pyridin-2(3H)-yl)acetamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.0004
N-cyclopropyl-1-methyl-3-oxo-1,3-dihydro-2,1-benzothiazole-5-sulfonamide
-
60 mM KCl, 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 0.01% (w/v) bovine serum albumin, 0.01% (v/v) Triton X-100, at 20C
0.01
trihydroxy benzoyl biphenyl carboxylate hydrazone, trihydroxybenzoyl naphthyl hydrazone
A1Z651
IC50 above 0.01 mM, with RNA-DNA hybrid HTS-1 as substrate, at pH 7.8 and 37C; IC50 above 0.01 mM, with RNA-DNA hybrid HTS-2 as substrate, at pH 7.8 and 37C
-
0.01
7-(furan-2-yl)-2-hydroxy-isoquinoline-1,3(2H,4H)-dione
A1Z651
IC50 above 0.01 mM, with RNA-DNA hybrid HTS-1 as substrate, at pH 7.8 and 37C; IC50 above 0.01 mM, with RNA-DNA hybrid HTS-2 as substrate, at pH 7.8 and 37C
-
additional information
additional information
-
no inhibitory activity against human RNase H1 for 5-nitrofuran-2-carboxylic acid adamantan-1-carbamoyl methyl ester
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.000038
-
-
0.001
-
below, mutant D97A, with 50 mM Mg2+ or 10 mM Mn2+
0.0046
-
mutant E98A, with 10 mM Mn2+
0.0051
-
mutant E98A, with 10 mM Mg2+
0.03
-
mutant D202A, with 10 mM Mn2+
0.04
-
purified mutant Y46A, in presence of Mn2+, pH 8.5, 30C
0.046
-
mutant D202A, with 10 mM Mg2+
0.046
-
purified mutant Y46A, in presence of Mg2+, pH 8.5, 30C
0.057
-
isozyme RNase H1beta, with Mn2+
0.06
-
purified mutant Q54A, in presence of Mn2+, pH 8.5, 30C
0.068
-
purified mutant Q54A, in presence of Mg2+, pH 8.5, 30C
0.07
-
isozyme RNase H1beta, with Mg2+
0.3
-
mutant E232A, with 10 mM Mn2+
0.31
P10442
15C, pH 8.5, purified recombinant enzyme
0.42
-
mutant E232A, with 10 mM Mg2+
0.48
Q9X122
substrate M13 DNA/RNA hybrid, enzyme mutant W22A, pH 9.0, 30C, in presence of 50 mM KCl
0.55
-
purified mutant S48A, in presence of Mn2+, pH 8.5, 30C
0.59
-
purified mutant L52A, in presence of Mg2+, pH 8.5, 30C
0.61
-
purified mutant S48A, in presence of Mg2+, pH 8.5, 30C
0.75
-
recombinant soluble nontagged enzyme
1.1
P0A7Y4
purified mutantE48A, at 10 mM MnCl2
1.1
P10442
30C, pH 8.5, purified recombinant enzyme
1.1
-
wild-type enzyme, with 10 mM Mn2+
1.1
-
purified wild-type enzyme, in presence of Mn2+, pH 8.5, 30C
1.2
-
purified mutant K50A, in presence of Mn2+, pH 8.5, 30C
1.5
P0A7Y4
purified mutant E48A/D134N at 10 mM MnCl2
1.5
-
purified mutant V42A, in presence of Mg2+, pH 8.5, 30C
1.6
-
purified mutant K50A, in presence of Mg2+, pH 8.5, 30C
1.9
-
wild-type enzyme, with 50 mM Mg2+
1.9
-
purified wild-type enzyme, in presence of Mg2+, pH 8.5, 30C
2.1
-
isozyme RNase H1alpha, with Mn2+
3.4
Q8EE30
mutant N29K/D39G/M76V/K90N/R97G/D136H, 30C
3.6
Q9X122
substrate M13 DNA/RNA hybrid, wild-type enzyme, pH 9.0, 30C, in presence of 50 mM KCl
4.7
P0A7Y4
purified wild-type enzyme, at 1 mM MnCl2
4.9
P0A7Y4
purified wild-type enzyme, at 10 mM MnCl2
5.1
Q8EE30
mutant D136H, 30C; mutant N29K/D39G/M76V/K90N/R97G, 30C
5.5
Q8EE30
mutant N29K/D39G/M76V/K90N, 30C
7
-
isozyme RNase H1alpha, with Mg2+
7.6
Q25C12
15C, pH 8.5, purified recombinant enzyme
7.7
Q8EE30
mutant R97G, 30C
7.8
Q8EE30
wild-type, 30C
15.2
P0A7Y4
purified wild-type enzyme, at 0.0005 mM MnCl2
22
Q25C12
30C, pH 8.5, purified recombinant enzyme
24.2
P0A7Y4
purified mutant D134N, at 10 mM MnCl2
50.83
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
-
additional information
-
activity of wild-type and mutant enzymes at different temperatures
additional information
-
determination of RNA levels
additional information
-
the activity of the recombinant soluble enzyme is slightly higher than that of the recombinant refolded enzyme
additional information
-
reaction velocity at oxidizing and reducing conditions
additional information
-
activity of wild-type and mutant enzymes, determination by spectrophotometric assay, at different temperatures
additional information
-
development and validation of a CpRNase HII-based method for activity assay and detection: DNA-rN1-DNA fragments are modified with a fluorophore at the 5'-end and a quencher at the 3'-end to generate molecular beacons, which hybridize with single-stranded DNA to be cleaved by CpRNase HII, the method is suitable for large-scale genotyping, overview
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5
-
the logarithm of the turnover number of the enzyme increases steeply with pH until a pH-independent region is reached close to neutrality, the pH-dependence of log 1/KM is a sigmoidal curve reaching a maximal value at higher pH, suggesting deprotonation of a residue stabilises substrate binding
7.4 - 8.8
-
in presence of 0.5 mM Mn2+, enzyme form HA1
7.5 - 10
-
Mg-dependent hydrolysis activity by Tm-RNase H2 gradually increases from pH 7.5 to 10 without reaching a maximum
7.5 - 8
-
Tris buffer or potassium phosphate buffer
7.5 - 9.1
-
-
7.5
-
in presence of 40 mM Mg2+, enzyme form HB2
7.5
-
enzyme form H-2
7.5
-
in Hepes buffer
7.6
-
in presence of 0.5 mM Mn2+, enzyme form HA2, HB1 and HB2
7.7
-
in presence of 40 mM Mg2+, enzyme form HB1
7.8 - 7.9
-
assay at
7.8
-
assay at
7.8
-
assay at
7.9
-
assay at
8 - 8.5
-
in presence of 10 mM Mg2+
8 - 9
-
-
8
-
Mn2+-dependent enzyme
8
P0A7Y4
assay at
8
-
at 10 mM Mn2+ or Mg2+, wild-type enzyme
8
O29634
assay at
8
-
assay at
8
-
assay at
8
-
assay at
8
Q9CWY8
assay at
8.2 - 8.8
Q5TBB1, Q8TDP1
-
8.3
-
in presence of 5 mM Mg2+, enzyme form HA1
8.4
-
enzyme form H-1
8.5 - 9
-
-
8.5 - 9.5
-
cleavage of M13 DNA/RNA hybrid
8.5
-
Mn2+-dependent enzyme
8.5
-
Mn-dependent activity of Tm-RNase H2 is the highest at around pH 8.5
8.5
-
the standard cleavage reaction is performed at a pH of 8.5 in the presence of 1 mM MgCl2 or MnCl2, because at a higher pH range, the solubility of divalent metal ions decreases and RNA/DNA substrates might become destabilized
8.6
-
in presence of 5 mM Mg2+, enzyme form HA2
9
-
Mg2+-dependent enzyme
9
-
Mg2+-dependent enzyme
9
Q9X122
assay at
9
Q9YET5
assay at
9.5
-
Mg2+-dependent enzyme
9.8
-
above
10
P10442
-
10
Q25C12
-
10
-
the cleavage activity increases exponentially as the pH increases from 6 to 10
11
Q9YET5
-
additional information
-
folding/unfolding and metal binding at different pH values
additional information
-
the type 2 RNase H is an Mg2+- and alkaline pH-dependent enzyme
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 10
-
the cleavage activity increases exponentially as the pH increases from 6 to 10
6 - 11
E0X765
the enzyme exhibits approximately 80% of the maximal activity at pH 8.5
6.5 - 11
-
more than 60% activity at pH 6.5, about 70% activity at pH 7.0, maximum activity at pH 7.5, more than 80% activity between pH 8.0 and 11.0
6.5 - 8
-
in presence of 10 mM Mn2+ the wild-type enzyme shows maximal activity at pH 8.0, 58% activity at pH 6.5, no activity at pH 5.5
6.5 - 8
-
-
6.8 - 8.4
-
pH 6.8: about 60% of maximal activity, pH 8.4: about 35% of maximal activity, enzyme form H-2
6.9 - 9.1
-
pH 6.9: 50% of maximal activity, pH 7.5-9.1: optimum
7 - 10.5
-
pH 7.0: about 50% of maximal activity, pH 10.5: about 60% of maximal activity
7 - 11
O67644
the enzyme exhibits approximately 20-30% of maximal activity at pH 7.0 and 11.0
7 - 9.8
-
enzyme is inactive below pH 7.0, activity increases with increasing pH
7.1 - 12
P10442
-
7.1 - 12
Q25C12
-
7.5 - 10
-
activity range dependent on cation added
7.5 - 9
-
about 45% of maximal activity at pH 7.5 and at pH 9.0, enzyme form H-1
additional information
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
21
-
assay at
21
-
assay at
22
-
about, assay at room temperature
22
-
assay at
24
-
assay at
30
P0A7Y4
assay at
30
-
assay at
30
O29634
assay at
30
-
assay at, substrate RNA*DNA hybrid
30
Q9X122
assay at
30
Q9YET5
assay at
37
-
assay at
37
-
assay at
37
-
assay at
40
Q25C12
-
45
P10442
-
50
-
DNA-C135-linked mutant, substrate PPT-RNA
65
-
assay at, substrate PPT-RNA
65
-
wild-type enzyme, assay at, substrate PPT-RNA, DNA-C135-linked mutant enzyme shows optimal activity with this substrate at 65C
70
Q9YET5
-
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
15 - 60
P10442
-
15 - 60
Q25C12
-
20 - 70
-
-
25 - 70
-
activity profile
30 - 70
Q6L6Q4
and above, temperature profile
50 - 90
Q9YET5
50C: about 60% of maximal activity, 90C: about 40% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.6
Q6L6Q4
sequence calculation
9.5
-
calculated from sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
prostate cancer cell line, high level in enzyme type 1 and 2 activity
Manually annotated by BRENDA team
-
embryonal kidney cell line, high level in enzyme type 1 activity, low level in enzyme type 2 activity
Manually annotated by BRENDA team
-
cervical carcinoma cell line, high level in enzyme type 1 activity, moderate level in enzyme type 2 activity
Manually annotated by BRENDA team
-
rhabdomyosarcoma cell line, low level in enzyme type 1 and 2 activity
Manually annotated by BRENDA team
-
primarily concentrated in the germinal vesicle, around 5% of the activity is detected in the cytoplasm
Manually annotated by BRENDA team
-
thymidine kinase 1-deficient osteosarcoma cell line
Manually annotated by BRENDA team
Daucus carota GD-2
-
-
-
Manually annotated by BRENDA team
-
bladder carcinoma cell line, low level in enzyme type 1 activity, moderate level in enzyme type 2 activity
Manually annotated by BRENDA team
-
pancreatic carcinoma cell line, low level in enzyme type 1 activity, high level in enzyme type 2 activity
Manually annotated by BRENDA team
additional information
-
90% purified recombinant enzyme
Manually annotated by BRENDA team
additional information
-
developmental stage-specific expression from L3 to adult stage of RNAse H1 isozymes with different substrate specificities and divalent cation requirements, overview
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
enzyme HI, 5% of the activity
Manually annotated by BRENDA team
-
three isoenzymes: C-1, C-2, C-3
Manually annotated by BRENDA team
-
enzyme HI, primarily concentrated in
Manually annotated by BRENDA team
Q8WR57
the enzyme contains a mitochondrial targeting sequence with the first 40 amino acid residues at the N-terminus, the enzyme is imported into mitochondrial vesicles in vitro, the enzyme is processed after entry into mitochondria
Manually annotated by BRENDA team
Q8WSZ0
the enzyme contains a mitochondrial targeting sequence with the first 40 amino acid residues at the N-terminus, the enzyme is imported into mitochondrial vesicles in vitro, the enzyme is processed after entry into mitochondria
Manually annotated by BRENDA team
-
large-MW enzyme form
Manually annotated by BRENDA team
-
nucleoplasm and nucleoli
Manually annotated by BRENDA team
-
ribonuclease H I
Manually annotated by BRENDA team
-
isoenzyme C-2 is originally present in the nucleus and is released into cytosol because of its loose binding to the nuclear components
Manually annotated by BRENDA team
-
enzyme contains a nuclear-targeting domain
Manually annotated by BRENDA team
-
type 2 enzyme, restricted to, except in cell line 15PC3
Manually annotated by BRENDA team
-
nuclear RNase H1
Manually annotated by BRENDA team
Tetrahymena pyriformis GI
-
-
-
Manually annotated by BRENDA team
-
mitochondrial RNase H1
Manually annotated by BRENDA team
additional information
-
enzyme HII is cryptic
-
Manually annotated by BRENDA team
additional information
-
extranuclear
-
Manually annotated by BRENDA team
additional information
-
multiple form of ribonuclease H exists in different regions of the rat liver cell
-
Manually annotated by BRENDA team
additional information
-
enzyme type 1 of all cell lines and enzyme type 2 of 15PC3 are distributed throughout the whole cell, presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
-
Manually annotated by BRENDA team
additional information
-
translation initiates at each of the two in-frame AUGs of the Rnaseh1 mRNA, with the longer form being imported into mitochondria, subcellular localization study, overview
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Aquifex aeolicus (strain VF5)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli O139:H28 (strain E24377A / ETEC)
Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
Human immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus type 1 group M subtype B
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Shewanella oneidensis (strain MR-1)
Shewanella oneidensis (strain MR-1)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Xenotropic MuLV-related virus
Xenotropic MuLV-related virus
Xenotropic MuLV-related virus
Xenotropic MuLV-related virus
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
12800
-
intermediate mimic, ultracentrifugation experiments
693672
13000
-
intermediate mimic, gel filtration
693672
13000
-
gel filtration
720573
19000
-
gel filtration
730927
20700
-
ribonuclease H2, gel filtration
134077
21000
-
gel filtration
134403
21000
E0X765
gel filtration
729733
22000
-
recombinant soluble non-tagged enzyme, gel filtration
655904
23000
-
ribonuclease H IIa, gel filtration
134412
24000
-
SDS-PAGE
134080
25000
Q25C12
recombinant enzyme, gel filtration
664911
27000
-
gel filtration
729712
28000
-
ribonuclase H IIa, sucrose density gradient centrifugation
134412
32000
-
gel filtration
729712
33000
-
gel filtration
134406
35000
-
isoenzyme C-2, gel filtration
134388
35000
-
Mg2+-dependent enzyme, gel filtration
134389
36000 - 40000
-
enzyme form H2, gel filtration
134399
36000
-
gel filtration
134387
36000
Q6L6Q4
recombinant enzyme, gel filtration
664359
40000
-
glycerol density gradient centrifugation
134375
40000
-
Mg2+-dependent enzyme, gel filtration
134392
40300
-
ribonuclease H(42), gel filtration
134383
45000
-
enzyme HI, sucrose density gradient centrifugation
134408
63000
-
sucrose density gradient centrifugation
134368
64000
-
gel filtration
134368, 134370
67000
-
sucrose density gradient centrifugation
134380
67000
-
enzyme HII, sucrose density gradient centrifugation
134408
68000
-
sucrose density gradient centrifugation
134373
76000
-
sedimentation equilibrium analysis
134367
80000
-
calculation from sedimentation behavior
134371
89000
-
sucrose density gradient centrifugation
134409
100000 - 130000
-
gel filtration
134397
105000 - 110000
-
enzyme form H1, gel filtration
134399
110000
-
gel filtration
134380
110000
-
isoenzyme C-1 and C-3, gel filtration
134388
120000 - 125000
-
gel filtration, sucrose density gradient centrifugation
134386
120000
-
Mn2+-dependent enzyme, gel filtration
134392
140000 - 150000
-
gel filtration
134373
140000
-
Mn2+-dependent enzyme, gel filtration
134394
180000
-
Mg2+-dependent enzyme, gel filtration
134394
additional information
-
the apparent higher molecular weight obtained by gel filtration compared to sucrose density gradient centrifugation is probably caused by asymmetry of the enzyme protein
134380
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
Q8U036
x * 26000, SDS-PAGE
?
Q9HSF6
x * 24000, SDS-PAGE
?
-
x * 33000, enzyme form H2, SDS-PAGE
?
-
x * 21000, ribonuclease H2, SDS-PAGE
?
Q8WR57
x * 53000, about, enzyme precursor, sequence calculation, x * 49000, processed enzyme, SDS-PAGE
?
Q8WSZ0
x * 53000, about, enzyme precursor, sequence calculation, x * 49000, processed enzyme, SDS-PAGE
?
-
x * 30000, about, mitochondrial RNase H1, SDS-PAGE
?
-
x * 25300, calculated from sequence
?
Halobacterium salinarum NRC-1
-
x * 24000, SDS-PAGE
-
heterotrimer
Q9CWY8
arrangement of subunits to form an enzymatically active complex, structure of the heterotrimeric RNase H2 complex, overview
monomer
E0X765
1 * 24000, SDS-PAGE
monomer
-
2 * 68000, SDS-PAGE
monomer
-
1 * 21000, SDS-PAGE
monomer
-
1 * 23000, ribonuclease H IIa, SDS-PAGE
monomer
-
1 * 68000, enzyme HI, SDS-PAGE, 1 * 32000, HI enzyme, SDS-PAGE
monomer
-
1 * 43000 + 1 * 85000, SDS-PAGE
monomer
-
1 * 23000, recombinant soluble non-tagged enzyme, SDS-PAGE
monomer
Q25C12
1 * 25000, recombinant enzyme, SDS-PAGE
monomer
Q6L6Q4
1 * 33734, amino acid sequence calculation, 1 * 36000, recombinant enzyme, SDS-PAGE
monomer
-
enzyme is composed of five alpha-helices (A to E) and five beta-strands (I to V). The intermediate mimic is a monomer
monomer
-
1 * 16812, calculated from sequence
monomer
-
1 * 18000, calculated from amino acid sequence
monomer
E0X765
1 * 23800, calculated from amino acid sequence
monomer
-
1 * 26630, SDS-PAGE
monomer
-
1 * 28892, SDS-PAGE
monomer
-
1 * 25000, recombinant enzyme, SDS-PAGE
-
monomer
Sulfolobus tokodaii 7
-
1 * 16812, calculated from sequence
-
tetramer
-
1 * 31600, A, + 2 * 26600, B, + 1 * 24800, C, + 1 * 24300, D, SDS-PAGE
trimer
-
2 * 31600, A, + 1 * 24800, immunological analysis after SDS-PAGE
trimer
-
heterotrimer of subunits H2A, H2B, H2C, SDS-PAGE and gel filtration
trimer
Q9CWY8
heterotrimeric complex of the RNase H2A, RNase H2B, and RNase H2C proteins, crystallization data
monomer
Thermotoga maritima DSM 3109
-
1 * 26630, SDS-PAGE
-
additional information
-
polypeptides B and D found in the most purified fractions are shown to be generated during the early steps of the purification, are shown to be generated during the early steps of the purification procedure, suggesting specific protein nicking which does not affect the native molecular weight of the enzyme
additional information
-
determination of the stability of residues in different secondary structures, alpha-helices and beta-strands, of the enzyme, comparison of experimental and computational data, correlation of stability in alpha-helices and beta-strands
additional information
-
domain organization, the nuclear targeting, which also binds RNA, and the catalytic domains are localized distinctly to the N-terminal and C-terminal parts bound by a spacer domain
additional information
-
enzyme folding pathway
additional information
-
helical content of the enzyme structure is 23%
additional information
-
three-dimensional structure of wild-type enzyme
additional information
O29634
two-domain architecture
additional information
-
identification and analysis of folding core and flexible regions, which are evolutionary conserved important for catalysis, conserved quantitative stability/flexibility relationships, QSFR, overview
additional information
-
modeling and analysis of mutant enzymes structures with bound DNA/RNA hybrid substrates, overview
additional information
-
the enzyme contains a TBP-like substrate-binding domain at the N terminus
additional information
-
RNase H1 contains an N-terminal domain known as dsRHbd for binding both dsRNA and RNA/DNA hybrid
additional information
-
RNase HIII consists of the N-terminal domain and C-terminal RNase H domain, the enzyme contains a TBP-like substrate-binding domain at the N terminus
additional information
-
the enzyme shows a mixed beta-sheet with asymmetric alpha helices, and contains the C-helix, or basic loop, structure comparisons, overview
additional information
-
the RNase HII contains a regulatory C-terminal tail. The C-terminus might form a short alpha-helix in which two residues, I195 and L196, are essential for the cleavage activity. The C-terminal alpha-helix is likely involved in the Mn2+-dependent substrate cleavage activity through stabilization of a flexible loop structure
additional information
Q9X122
Tma-RNase HI contains a hybrid binding domain at the N-terminal region. Analysis for interaction between the C-terminal and the hybrid binding domains, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
Q8WR57
the enzyme is procesed after import into mitochondria
proteolytic modification
Q8WSZ0
the enzyme is procesed after import into mitochondria
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, using 0.2 m sodium citrate tribasic dehydrate, pH 8.3, and 20% (w/v) polyethylene glycol 3350, at 4C
O67644
crystallization of 40 mg/ml purified recombinant wild-type type 2 enzyme, and of recombinant selenomethionine enzyme mutant, with or without bound metal ions, hanging drop vapour diffusion method, mixing with equal volume of precipitant solution containing 10% PEG monomethylether 5000, 10% butanol, 20 mM sodium citrate, 100 mM Tris, pH 8.5, 3 days, formation of a cobalt-hexammine chloride complex, X-ray diffraction structure determination and analysis at 1.95-2.7 A resolution
O29634
vapor diffusion at room temperature, crystal structures of Archaeoglobus fulgidus RNase HII in complex with proliferating cell nuclear antigen (PCNA)
O29912
crystallization of a ternary complex of the DNA (containing 2'-deoxy-6-selenoguanosine), RNA and RNase H
-
purified recombinant mutant enzymes, with bound metal ions, sitting drop vapour diffusion method, 4C, 25-30% 2-metyl-2,4-pentanediol, as precipitant, 0.25 M ammonium acetate or 0.2 M NaCl, sodium citrateat pH 5.6, Tris at pH 7.0, or HEPES at pH 7.5, Microseeding with mutant D132N, nick phosphorylation and 20% ethanol at pH 7.0 for mutant E188A, soaking of crystals in solution containing Mg2+, Mn2+, or Ca2+ for 4-24 h, X-ray diffraction structure determination and analysis at 1.5-2.2 A resolution
-
mutant C33A/C63A/C133A to 1.6 A resolution. Space group P1
Q93SU7
4-10 mg/ml purifed recombinant wild-type and mutant D10A enzymes, in 20 mM HEPES, pH 7.0-8.0, 5-15% PEG 3350, hanging drop vapour diffusion method and microseeding, several weeks, X-ray diffraction structure determination and analysis
-
crystal structure analysis, overview
-
purified recombinant enzyme mutants with Mn2+ bound at the active sites, sitting drop vapour diffusion method, 6.7-9.9 mg/ml protein in 20 mM HEPES-NaOH, pH 7.0, 5-10 mm MnCl2, 20-28% PEG 3350, and 10% glycerol, 3 weeks, X-ray diffraction structure determination and analysis at 2.2-2.3 A resolution
-
RNase HI-dsRNA enzyme-inhibitor complexes with 9-mer and 10-mer RNA, sitting-drop vapor-diffusion method, 0.001-0.002 ml of 0.11-0.15 mM protein solution is mixed with an equal volume of reservoir solution containing 50 mM bis-Tris, pH 6.1, 12.5% PEG 3350, 25 mM NaCl, 2 mM MgCl2 and 1 mM TCEP, addition of 20 mM HEPES pH 8.0, 16% PEG 3350, molecular replacement, X-ray diffraction structure determination and anaylsis at 3.5-4.0 A resolution
-
purified recombinant enzyme, free or bound to Mg2+ or Mn2+, 6.4-8.0 mg/ml protein in 85 mM Tris-HCl, pH 8.5, 0.17 M lithium sulfate, 25.5% w/v PEG 4000, and 15% v/v glycerol, metal binding by soaking of crystals in 1 mM Mg2+ or Mn2+ containing solution for 24 h, heavy atom derivatization with 10 mM CH3HgCl or K2PtCl6, X-ray diffraction structure determination and analysis at 2.1-2.6 A resolution, modeling; RNase HIII in both metal-free and metal-bound form, 6.4-8.0 mg/ml protein, native enzyme crystals from 85 mM TrisHCl, pH 8.5, 0.17 M lithium sulfate, 25.5% w/v PEG 4000, and 15% v/v glycerol, soaking of crystals in a solution containing 50 mM Mg2+ or Mn2+, preparation of heavy-metal derivatives, X-ray diffraction structure determiation and analysis at 2.1-2.6 A resolution, modelling
-
purified recombinant mutant Q54A-RNase H3 enzyme, X-ray diffraction structure determination and analysis at 2.6 A resolution
-
analysis of the crystal structure of human RNase H1 in complex with a DNA/RNA duplex
-
crystal structure analysis, overview
-
purified recombinant subunts in a complex containing RNASEH2B residues 2-226, full-length RNASEH2C, and RNASEH2A with catalytic site mutations D34A and D169A, X-ray diffraction structure determination and analysis at 4.1-4.4 A resolution
Q9CWY8
recombinant deletion mutant AB14-233C, sitting drop vapor diffusion method at 18C, from 0.1 M MgCl2, 15% PEG 3350, 0.1 M Bis-Tris, pH 5.5, and 2 mM reduced glutathione, X-ray diffraction structure determination and analysis at 3.1 A resolution, molecular replacement
-
the enzyme's hybrid binding domain complexed with a 12 bp RNA-DNA hybrid and an 6 bp RNA-DNA hybrid, molecular replacement, hanging drop vapour diffusion method, 21C, 6 bp complex crystals are obtained with the well solution containing 10% PEG 3350, 0.2 M NaCl, 0.1 M Tris, pH 8.5, 12 bp complex crystals are obtained with 1.2 M NaCl and 0.1 M HEPES, pH 7.5, X-ray diffraction structure determination and anaylsis at 2.7-2.8 A and 2.1-2.2 A resolution, respectively
-
heterotrimeric complex of the RNase H2A, RNase H2B, and RNase H2C proteins, to 3.1 A resolution. The overall structure reveals an elongated arrangement of the subunits with the H2C protein in the middle flanked by the H2A and H2B proteins on the ends. Construction of a model for an Okazaki fragment binding to the mouse RNase H2 complex. In the model, the double-stranded RNA-DNA molecule runs through the active site cleft and is positioned to make several favorable electrostatic interactions and no significant steric clashes with the protein. The RNA-DNA hybrid is situated so that the target phosphodiester bond is in the proper orientation for nucleophile attack initiated by a two-metal ion chemistry
Q9CWY8
fusion protein of maltose binding protein and the N-terminal RNase H domain, to 2.2.5 A resolution. Protein is monomeric in solution but associates in the crystal to form a dimer
P9WLH5
three-dimensional structural model of RNase HII complexed with its substrate, suggests that the amino acids D110, R113 and F114 are located in the region that discriminates DNA from RNA in the non-substrate strand of RNA-RNA
Q8U036
N29K/D39G/M76V/K90N/R97G/D136H mutant, to 2.5 A resolution. The main chain fold and interactions of the side-chains of the RNase HI protein are basically identical to those of the wild-type protein, except for the mutation sites. The mutations independently affect the protein structure, and the thermostabilizing effects of the mutations are roughly additive
Q8EE30
purified recombinant enzyme Sa-RNase HIII, sitting drop vapour diffusion method, 0.004 ml of 3.2 mg/ml protein in PBS containing 137 mM NaCl, 2.7 mM KCl, 10 mM sodium phosphate dibasic, 2 mM potassium phosphate monobasic, pH 7.4, is mixed with 0.002 ml of precipitation solution containing 0.17 M ammonium sulfate, 25.5% w/v PEG 8000, 15% v/v glycerol, and 0.085 M sodium cacodylate pH 6.5, X-ray diffraction structure determination and analysis at 2.59-2.70 A resolution
-
crystal structure is determined at 1.6 A resolution, crystals are grown by the sitting-drop vapor-diffusion method at 4C
-
crystals are grown at 4C by the sitting-drop vapour-diffusion method. Native X-ray diffraction data are collected to 1.5 A resolution using synchrotron radiation from station BL41XU at SPring-8. The crystal belongs to space group P4(3), with unit-cell parameters a = b = 39.21, c = 91.15 A
-
purified recombinant wild-type enzyme, X-ray diffraction structure determination and analysis at 1.66-1.72 A resolution
-
purified truncated enzyme RNase HII-213, comprising residues 1-213, metal-bound or metal-free, hanging drop vapour diffusion method, 15% w/v PEG 6000, 200 mM MES, pH 6.5, X-ray diffraction structure determinaion and analysis at 3.5 A resolution
-
RNase H2 in complex with nucleic acid containing a 5'RNA-DNA3' junction, X-ray diffraction structure determination and analysis at 2.0 A resolution
-
sitting drop vapor diffusion method, using 100 mM TrisHCl pH 8.5, 200 mM MgCl2-6H2O and 30% (w/v) PEG 4000, at 4C
E0X765
sitting drop vapor diffusion method, using 27% (w/v) polyethylene glycol 1500 and 0.1 M sodium citrate, pH 4.7
A1Z651
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 8
-
unstable below pH 5.0 and above pH 8.0
134380
6 - 7
-
most stable at
134380
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
P10442
half-life about 45 min
664911
30
Q25C12
half-life about 30 min
664911
30.4
Q8EE30
Tm of wild-type
708487
35
-
50% loss of activity after 45 s
134380
35.8
Q8EE30
Tm of mutant R97G
708487
40.1
Q8EE30
Tm of mutant D136H
708487
46.2 - 76.5
Q9HSF6
the melting temperature in the presence of 300 mM MgCl2, 20 mM MnCl2, 3 M NaCl, or 300 mM MgCl2 plus 3 M NaCl is 46.2C, 50C, 66.9C, and 76.5C, respectively
729744
48.2
-
melting temperature in presence of 1.2 M guanidinium hydrochloride
134403
49.1
Q8EE30
Tm of mutant N29K/D39G/M76V/K90N
708487
50
-
50% loss of activity after 43 min
134375
50
-
DNA-linked mutant, loss of 50% activity after 15 min
657218
52.5
Q8EE30
Tm of mutant N29K/D39G/M76V/K90N/R97G
708487
53.1
-
melting temperature
729712
55
-
10 min, 60% loss of activity
134403
55
Q6L6Q4
half-life 10 min
664359
59.2
Q8EE30
Tm of mutant N29K/D39G/M76V/K90N/R97G/D136H
708487
60
-
DNA-linked mutant, complete inactivation after 15 min
657218
66.1
-
melting temperature
729712
66.5
Q93SU7
Tm, cysteine-free mutant C33A/C63A/C133A
707499
68.5
Q93SU7
Tm, wild-type
707499
70
-
neither Chlamydophila pneumoniae RNase HII nor Chlamydophila pneumoniae RNase HIII is thermostable
681805
70
Q9YET5
fully stable at 70C for at least 10 min under assay condition containing 100 mM MgCl2. Under the assay condition containing 10 mM MgCl2, little activity can be detected
726556
75
-
melting temperature curve of the intermediate mimic shown. The heat denaturation experiment shows that this intermediate mimic unfolds cooperatively as temperature increases, with a melting temperature (Tm) of about 75C
693672
78
-
Tm-value for mutant enzyme DELTAC6
718846
82.1
-
melting temperature in presence of 1.2 M guanidinium hydrochloride
134403
90
-
10 min, stable
134403
90
-
DNA-linked mutant is almost fully stable after 15 min
657218
93
-
Tm-value for mutant enzyme C58/145A
718846
102
-
Tm-value for wild-type enzyme. The thermostable protein is destabilized by elimination of the disulfide bond and C-terminal truncation
718846
additional information
-
structures and mechanism of thermostability
657146
additional information
-
melting temperature is 66C, conserved quantitative stability/flexibility relationships, QSFR, thermodynamics, thermal stability and flexibility of the enzyme
666879
additional information
-
melting temperature is 86C, conserved quantitative stability/flexibility relationships, QSFR, thermodynamics, thermal stability and flexibility of the enzyme
666879
additional information
-
melting temperatures for duplexes of antisense oligodeoxynucleotide with RNA-15 and RNA-20 were 63C and 70C, respectively
677553
additional information
-
analysis of thermal unfolding, the folding core of Chlorobium tepidum RNaseH plays an important role in the unfolded state of this protein
714194
additional information
-
analysis of thermal unfolding, the folding core of Thermus thermophilus RNaseH plays an important role in the unfolded state of this protein
714194
additional information
-
comparison of thermostability of wild-type and mutant enzymes, overview
715581
additional information
-
the C-terminal of RNase HI from the hyperthermophile Sulfolobus tokodaii does not affect overall structure, and thermal stabilization is caused by local interactions of the C-terminal, suggesting that the C-terminal residues could be used as a stabilization tag. Thermodynamic measurements of the stability of variants lacking the disulfide bond, C58/145A, or the six C-terminal residues (DELTAC6) and by structural analysis of DELTAC6, overview
716693
additional information
-
the C-terminus tail (G144-T149) of the RNase HI plays an important role in hyperstabilization of this protein
725763
additional information
Q9YET5
stabilization of the thermostable enzyme is enhanced with increased salt concentration (Mg2+ or K+)
726556
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
denaturation kinetics, midpoint at about 1.8 M urea and 5C
P10442
metal binding stabilizes the enzyme by decreasing its unfolding rate, mechanism
-
metal ion and substrate stabilize the enzyme
P10442
the N-terminal extension of the enzyme functions as a substrate-binding domain and stabilizes the RNase H domain
-
partially purified enzyme extract is labile against freezing and dilution, addition of 45% glycerol
-
denaturation kinetics, midpoint at about 1.6 M urea and 5C
Q25C12
metal ion and substrate stabilize the enzyme
Q25C12
ribonuclease H2 from Thermococcus kodakarensis is stabilized by its remarkably slow unfolding rate in guanidine hydrochloride, making the native state of RNase H2 completely resistant to subtilisin
-
the C-terminal extension of the enzyme functions as a substrate-binding domain and stabilizes the RNase H domain
-
calculation of stability versus hydrophobicity and residue contacts
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 0.025 mg enzyme per ml, in 0.1 M Tris-HCl, pH 7.5, 0.01 MgCl2, 20 mM urea, 1 mM DTT, 0.1% Triton X-100, 50% v/v glycerol, stable for several weeks
-
-20C, 25 mM Tris-HCl, pH 7.5, 30 mM NaCl, 0.5 mM EDTA, 5 mM 2-mercaptoethanol, 50% glycerol, stable
-
-70C, complete loss of activity after a few days
-
-20C, 50% v/v glycerol, stable for several months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HiTrap SP column chromatography and Hi-Trap heparin column chromatography
O67644
recombinant enzymes from Escherichia coli
O29634
calf; two highly active enzyme forms: H1 and H2
-
large scale purification
-
recombinant His-tagged isozymes to near homogeneity from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant recombinant chimeric and point mutant enzymes from Escherichia coli strain BL21(DE3) by heparin affinity chromatography
-
one Mn2+-dependent RNase H and one Mg2+-dependent RNase H
-
natural and selenomethionyl recombinant enzyme
-
Ni-NTA column chromatography, DEAE-cellulose column chromatography, phosphocellulose P11 column chromatography, and heparin Sepharose column chromatography
-
recombinant insoluble enzyme in a urea-denatured form, recombinant soluble intein-tagged enzyme
-
recombinant mutant enzymes from strain HB101 by heparin affinity chromatography
-
recombinant RNase HII from strain BL21(DE3) to near homogeneity by a combination of ion exchange and affinity chromatography
-
strain B and strain D110
-
one Mn2+-dependent RNase H and one Mg2+-dependent RNase H
-
HiTrap Q column chromatography, HiTrap heparin column chromatography, and Superdex 200 gel filtration
-
recombinant enzyme to homogeneity from Escherichia coli strain MIC2067(DE3) by ammonium sulfate precipitation, heparin affinity chromatography, and gel filtration
Q6L6Q4
recombinant wild-type and mutant enzymes from Escherichia coli strain MIC2067(DE3)
-
HiTrap Q column chromatography, hydroxyapatite column chromatography, Mono Q column chromatography, and Superdex 200 gel filtration
Q9HSF6
His-Trap Ni-NTA column chromatography
-
recombinant enzyme; recombinant enzyme; recombinant enzyme
Q5TBB1, Q8TDP1
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His-tagged RNase H1 from Escherichia coli strain BL21(DE3) by nickel affinity and anion exchange chromatography followed by reverse phase chromatography
-
recombinant RNase H1 from Escherichia coli strain BL21(DE3) using affinity and ion exchange chromatography
-
recombinant wild-type and mutant enzymes from Escherichia coli BL21(DE3)
-
RNase H1
-
recombinant His-tagged RNAseHIIC from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
Q8WR57
recombinant His-tagged RNAseHIIC from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
Q8WSZ0
recombinant wild-type and mutant enzymes from Escherichia coli, partially
-
enzyme form H-1 and H-2
-
partial, two types of enzyme: H1 and H2
-
isoenzyme I, II and III
-
HiTrap heparin column chromatography
-
ribonuclease H2
-
recombinant enzyme from Escherichia coli strain MIC2067(DE3) to homogeneity by heparin affinity chromatography and gel filtration
Q25C12
recombinant N-terminally His-tagged RNase HIII from Escherichia coli strain BL21 CodonPlus (DE3) RIPL by nickel affinity chromatography, dialysis and cleavage of the His-tag by TEV protease
-
recombinant wild-type and truncated enzymes from Escherichia coli
-
HiTrap Q column chromatography, HiTrap heparin column chromatography, and Superdex 200 gel filtration
-
recombinant recombinant chimeric mutant enzyme from Escherichia coli strain BL21(DE3) by heparin affinity chromatography, and His-tagged mutant L56S by nickel affinitychromatography
-
recombinant wild-type and mutant enzymes from Escherichia coli
-
using Ni-NTA agarose and reverse-phase HPLC
-
recombinant GST-tagged wild-type and mutant enzymes from Escherichia coli
-
HiTrap SP column chromatography and HiTrap phenyl column chromatography
E0X765
GST column chromatography
A1Z651
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
Q9YET5
expressed in Escherichia coli MIC2067(DE3) cells
O67644
type 2 enzyme, overexpression of wild-type in Escherichia coli BL21(DE3), and of selenomethionine mutant in Escherichia coli strain B834, a methionine-auxotroph BL21(DE3) derivative
O29634
expression of mutant enzymes in Escherichia coli
-
genetic organization of the RNase H1-related gene family, different isozymes by alternative splicing, sequence comparisons of isozymes, overexpression of His-tagged isozymes in Escherichia coli strain BL21(DE3)
-
expression of RNase HII and RNase HIII in the enzyme-deficient Escherichia coli strain DY329, complementation assay, Chlamydophila pneumoniae RNase HII can complement both Escherichia coli RNase HII and RNase HI, but Chlamydophila pneumoniae RNase HIII can only complement the latter
-
expression in Escherichia coli
Q93SU7
expression of recombinant chimeric and point mutant enzymes in Escherichia coli strain BL21(DE3), I53 and L56 point mutants are expressed insolubly in inclusion bodies
-
gene rnhB, overexpression of the enzyme in an insoluble form in different strains of Escherichia coli, overexpression of soluble enzyme with a self-cleavable intein-tag
-
overexpression in strain BL21(DE3)
-
overexpression of mutant enzymes in strain HB101
-
overexpression of RNase HII in strain Bl21 (DE3)
-
overexpression of wild-type and mutant D10A enzymes in Escherichia coli
-
overexpression of wild-type and mutant enzyme
P0A7Y4
overexpression of wild-type and mutant enzymes in strain HB101
-
complementation assay using the enzyme-deficient Escherichia coli strain MIC2067, which shows an RNase H-dependent temperature-sensitive growth phenotype, by wild-type and mutant enzymes, no complementation by the C domian mutant, overview; gene rnhC, overexpression of the soluble enzyme in Escherichia coli strain MIC2067(DE3)
-
expressed in Escherichia coli MIC2067(DE3) cells
-
gene rnhC, DNA and amino acid sequence determination and analysis, overexpression of the soluble enzyme in Escherichia coli strain MIC2067(DE3)
Q6L6Q4
overexpression of wild-type and mutant enzymes in Escherichia coli strain MIC2067(DE3)
-
expressed in Escherichia coli BL21-CodonPlus(DE3) cells
Q9HSF6
expressed in Escherichia coli BL21(DE3)[pLysS] cells
-
expression in Escherichia coli and in HeLa cell; expression in Escherichia coli and in HeLa cell; expression in Escherichia coli and in HeLa cell
Q5TBB1, Q8TDP1
expression of enzyme type 1 and 2 as GFP-fusion proteins in all 6 cell lines, transfection of cell lines with antisense oligodeoxynucleotides directed against RNA polymerase II, replication protein A, and Ha-ras, determination of response in expression levels of the enzyme type 1 and 2, overview
-
expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
expression of His-tagged RNase H1 in Escherichia coli strain BL21(DE3)
-
expression of human RNase H1 in Escherichia coli
-
expression of wild-type and mutant enzymes in Escherichia coli BL21(DE3)
-
simultaneous expression of GST-tagged RNASEH2B, and untagged RNASEH2A and RNASEH2C subunits from vector pGEX6P1 as polycistronic construct, in Escherichia coli strain Rosetta-2
Q9CWY8
RNase HIIC, DNA and amino acid sequence determination and analysis, expression as His-tagged enzyme in Escherichia coli strain BL21(DE3), genetic complementation of a RNase-deficient Escherichia coli strain fails due to lacking processing of the inactive precursor protein
Q8WR57
RNase HIIC, DNA and amino acid sequence determination and analysis, expression as His-tagged enzyme in Escherichia coli strain BL21(DE3), genetic complementation of a RNase-deficient Escherichia coli strain fails due to lacking processing of the inactive precursor protein
Q8WSZ0
expression of wild-type and mutants enzymes in Escherichia coli BL21(DE3)
-
gene rnaseh1, translation initiates at each of the two in-frame AUGs of the Rnaseh1 mRNA, with the longer form being imported into mitochondria, regulation mechanisms, overview. Recombinant enzyme expression in Flp-In T-Rex-293 cells, and in vitro translation.
-
expression in Escherichia coli
P9WLH5
gene PAB0352
-
expression in Escherichia coli
Q8U036
expressed in Escherichia coli BL21(DE3) cells
-
gene rnhB, DNA and amino acid sequence determination and analysis, overexpression in Escherichia coli strain MIC2067(DE3), a rnhA/rnhB double mutant strain, as 60% soluble and 40% insoluble protein
Q25C12
overexpression of N-terminally His-tagged RNase HIII in Escherichia coli strain BL21 CodonPlus (DE3) RIPL
-
overexpression of wild-type and several truncated enzymes in Escherichia coli
-
expressed in Escherichia coli MIC2067(DE3) cells
-
expression of wild-type and truncated D107N mutant enzymes in Escherichia coli
-
RNase HI sequence comparisons, expression of wild-type and mutant enzymes in Escherichia coli
Q9X122
expression in Escherichia coli
-
expression of recombinant chimeric mutant enzyme and of His-tagged mutant L56S in Escherichia coli strain BL21(DE3)
-
gene rnhA, overexpression in Escherichia coli MIC3001 of wild-type and mutant enzymes, complementation of enzyme-dependent temperature-sensitive growth phenotype of the Escherichia coli host strain by expression of the wild-type enzyme, but only marginally by the mutant D134H
-
overexpression of wild-type and mutant enzymes in Escherichia coli strain HB101
-
expression of wild-type and N-terminally truncated mutant enzymes as GST-fusion proteins in Escherichia coli temperature sensitive mutant strain MIC3001
-
expressed in Escherichia coli BL21(DE3) cells
E0X765
expressed in Escherichia coli BL-21cells
A1Z651
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E194A
O67644
the mutant exhibits 20 and 35% of the Mg2+- and Mn2+-dependent activities of the wild type enzyme, respectively
E196A
O67644
the mutant shows 84.8% Mn2+-dependent and 63% Mg2+-dependent activities compared to the wild type enzyme
E198A
O67644
the mutant shows 76.1% Mn2+-dependent and 63% Mg2+-dependent activities compared to the wild type enzyme
Y45A
O67644
the mutant shows 47.8% Mn2+-dependent and 5.4% Mg2+-dependent activities compared to the wild type enzyme
D101N
O29634
mutation results in more than 95% decrease in activity compared to wild-type enzyme
D129A
O29634
Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 2.2fold higher than the wild-type value. The turnover number is 30% of the wild-type value
D129N
O29634
mutation results in about 75% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 70% of the wild-type value. The turnover number is 20% of the wild-type value
D167A
O29634
no loss of activity
D37A
O29634
mutation results in about 90% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 80% of the wild-type value. The turnover number is 5% of the wild-type value
D37N
O29634
mutation results in about 10% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 1.5fold higher than the wild-type value. The turnover number is 40% of the wild-type value
D6N
O29634
mutation results in more than 95% decrease in activity compared to wild-type enzyme
E7Q
O29634
mutation results in more than 95% decrease in activity compared to wild-type enzyme
K143A
O29634
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
K143A
O29634
mutation results in about 80% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 31.3fold higher than the wild-type value. The turnover number is 150% of the wild-type value
K39A
O29634
mutation results in about 30% decrease in activity compared to wild-type enzyme
R146A
O29634
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R146A
O29634
mutation results in more than 95% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 26.7fold higher than the wild-type value. The turnover number is 140% of the wild-type value
R188A
O29634
no loss of activity
R45A
O29634
mutation results in about 5% decrease in activity compared to wild-type enzyme
R46A
O29634
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R46A
O29634
mutation results in about 50% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 60fold higher than the wild-type value. The turnover number is 130% of the wild-type value
S139A
O29634
no loss of activity
S139A
O29634
mutation results in about 40% decrease in activity compared to wild-type enzyme
S38A
O29634
mutation results in about 35% decrease in activity compared to wild-type enzyme
Y164A
O29634
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
Y164A
O29634
mutation results in more than 95% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 44.7fold higher than the wild-type value. The turnover number is 160% of the wild-type value
D132N
-
site-directed mutagenesis, crystal structure analysis of the mutant bound to divalent metal ions
D132N
-
perturbs the coordination shell of the A-site Mg2+
D132N
-
the plasmid expressing Bacillus halodurans RNase H
D192N
-
site-directed mutagenesis, crystal structure analysis of the mutant bound to divalent metal ions
D192N
-
crystallographic model. Although the mutant enzyme is completely inactive, D192N substitution supposedly does not significantly affect the active site architecture
S94V
Chlamydia pneumoniae AR39
-
the mutation decreases the RNase H activity 3-6fold
-
C33A/C63A/C133A
Q93SU7
cysteine-free mutant, crystallization data
I53A
-
site-directed mutagenesis
I53D
-
site-directed mutagenesis
L56A
-
site-directed mutagenesis
L56D
-
site-directed mutagenesis
C13A/C63A/C133A/E135C
-
site-directed mutagenesis, 37% activity compared to the wild-type enzyme
D10A
-
site-directed mutagenesis, active site mutant, no metal binding, altered folding kinetics in absence of metal ions to the values for wild-type enzyme in presence of metal ions
D10A
P0A7Y4
site-directed mutagenesis, active site mutant, poor binding of Mn2+
D10A
-
mutation relieves charge repulsion in the periphery of the protein and stabilizes the protein by more than 3 kcal/mol. Comparison with mutant D10A/I53D, reference protein for three-state folding
D10A/I53D
-
mutations simultaneously destabilize the core and stabilize the periphery of the protein. Comparison with stabilized mutant D10A, reference protein for two-state folding
D10N
P0A7Y4
site-directed mutagenesis, active site mutant, 1700fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
D134A
P0A7Y4
site-directed mutagenesis, mutant shows activity in presence of Mn2+, activity is similar to the wild-type enzyme, but the mutant is not inhibited by Mn2+ concentrations above 0.1 mM in contrast to the wild-type enzyme, 5.0fold increased dissociation constants for binding of Mn2+
D134A/L87A
-
site-directed mutagenesis, crystal structure analysis with bound Mn2+
D134N
P0A7Y4
site-directed mutagenesis, mutant shows high activity in presence of Mn2+ without inhibition at higher Mn2+ concentrations, and 5.4fold increased dissociation constants for binding of Mn2+
D70N
P0A7Y4
site-directed mutagenesis, active site mutant, 440fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
E48A
P0A7Y4
site-directed mutagenesis, mutant shows activity in presence of Mn2+, activity is similar to the wild-type enzyme, but the mutant is not inhibited by Mn2+ concentrations above 0.1 mM in contrast to the wild-type enzyme, 10fold increased dissociation constants for binding of Mn2+
E48A/D134A
P0A7Y4
site-directed mutagenesis, active site mutant, highly reduced activity and 65fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
E48A/D134N
P0A7Y4
site-directed mutagenesis, active site mutant, reduced activity and 260fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
E48A/L87A
-
site-directed mutagenesis, crystal structure analysis with bound Mn2+
E48A/L87A/D134A
-
site-directed mutagenesis, crystal structure analysis with bound Mn2+
E48Q
P0A7Y4
site-directed mutagenesis, mutant shows activity in presence of Mn2+ and 9.2fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
D202A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme, site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
D97A
-
site-directed mutagenesis, inactive mutant, site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
E232A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
E98A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme, site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
K50A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Q54A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S48A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
V42A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Y46A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
D777A
-
the mutation in the RNase H domain of hepatitis B virus polymerase yields significantly reduced amounts of viral DNAs Minus-strand DNA synthesis is incomplete due to loss of catalytic activity of RNase H
R703A
-
the mutation in the RNase H domain of hepatitis B virus polymerase yields significantly reduced amounts of viral DNAs. Minus-strand DNA synthesis is incomplete due to loss of catalytic activity of RNase H
R781A
-
the mutation in the RNase H domain of hepatitis B virus polymerase yields significantly reduced amounts of viral DNAs. The minus-strand DNA synthesis is near complete to some extent, while the plus-strand DNA synthesis (i.e., relaxed circular DNA) is severely impaired due to the defect in RNase H activity
A177T
Q5TBB1, Q8TDP1
mutation in subunit H2B associated with Aicardi-Goutieres' syndrome, near-normal activity
A177T
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
A177T
Q9CWY8
naturally occuring mutation in subunit RNASEH2B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS. The mutation disrupts the interface between a RNASEH2B alpha-helix and the RNASEH2C kinked helix
C147A
-
site-directed mutagenesis, mutant is active under reducing and oxidizing conditions
C147A/C148A
-
site-directed mutagenesis, mutant is active under reducing and oxidizing conditions
C148A
-
site-directed mutagenesis, mutant is active under reducing and oxidizing conditions
C191A
-
site-directed mutagenesis, mutant is active under reducing conditions, but shows poor activity under oxidizing conditions
D169A
Q9CWY8
active site residue mutation in subunit RNASEH2A
D2Y/L3P
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
D34A
Q9CWY8
active site residue mutation in subunit RNASEH2A
D39Y
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
F230L
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
G185V
Q5TBB1, Q8TDP1
mutation in subunit H2B associated with Aicardi-Goutieres' syndrome, near-normal activity
G37S
Q5TBB1, Q8TDP1
mutation in subunit H2A associated with Aicardi-Goutieres' syndrome, greatly reduced activity and processivity
G37S
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
G83S
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
H264A
-
the mutation causes an about 100fold decrease in kcat under multiple-turnover conditions, but does not alter the Km value. The H264A mutant is not rescued by increasing the Mg2+ concentration to 80 mM
H86R
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K143I
Q5TBB1, Q8TDP1
mutation in subunit H2C associated with Aicardi-Goutieres' syndrome, near-normal activity
K143I
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K143I
Q9CWY8
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K162T
Q5TBB1, Q8TDP1
mutation in subunit H2B associated with Aicardi-Goutieres' syndrome, near-normal activity
K162T
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K59A/K60A
-
site-directed mutagenesis in the hybrid binding domain, the mutation abolishes dsRNA binding
L138F
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P138L
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P138L
Q9CWY8
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P151S
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P151S
Q9CWY8
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P43H
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P76L
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P76L
Q9CWY8
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R108W
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R13H
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R186W
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R235Q
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R291H
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R291H
Q9CWY8
naturally occuring mutation in subunit RNASEH2A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R32A/R33A
-
site-directed mutagenesis in the hybrid binding domain outside of the interface, the mutation abolishes dsRNA binding
R35A
-
site-directed mutagenesis, the mutant shows a much lower specific activity than the wild-type enzyme
R57A
-
site-directed mutagenesis in the hybrid binding domain on the observed nucleic-acid interface, the mutation abolishes dsRNA binding
R69W
Q5TBB1, Q8TDP1
mutation in subunit H2C associated with Aicardi-Goutieres' syndrome, 30-40% of wild-type activity
R69W
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R69W
Q9CWY8
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R72A/K73A
-
site-directed mutagenesis in the hybrid binding domain outside of the interface, the mutation abolishes dsRNA binding
S159I
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
S229P
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
T163I
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
T240M
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
V183M
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
V185G
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
W43A
-
site-directed mutagenesis in the hybrid binding domain on the observed nucleic-acid interface, the mutation abolishes dsRNA binding, the mutant shows a much lower specific activity than the wild-type enzyme
W73L
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
Y219H
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
D112N
-
site-directed mutagenesis, 0.17% activity compared to the wild-type enzyme, no Mn2+ binding
D149N
-
site-directed mutagenesis, 0.12% activity and slightly weakened Mn2+ binding properties compared to the wild-type enzyme
D7N
-
site-directed mutagenesis, 0.13% activity and slightly weakened Mn2+ binding properties compared to the wild-type enzyme
E8Q
-
site-directed mutagenesis, 0.14% activity and slightly weakened Mn2+ binding properties compared to the wild-type enzyme
D142N
Q9CWY8
mutation in strictly positionally conserved acidic residues, complete loss of activity
D170N
Q9CWY8
mutation in strictly positionally conserved acidic residues, complete loss of activity
D34N
Q9CWY8
mutation in strictly positionally conserved acidic residues, complete loss of activity
E35A
Q9CWY8
mutation in strictly positionally conserved acidic residues, complete loss of activity
A115E
Q8U036
partially enhanced nuclease activity for the RNA-DNA duplex substrate
F114E
Q8U036
reduced nuclease activity respectively for the RNA-DNA duplex substrate
R113E
Q8U036
partially reduced nuclease activity respectively for the RNA-DNA duplex substrate
G42S
-
the mutant shows strongly reduced activity compared to the wild type enzyme
I183M
-
site-directed mutagenesis in the polymerase domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
M520I
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
N398D
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
P45D/Y219A
-
the mutant shows strongly reduced activity compared to the wild type enzyme
P45E/Y219A
-
inactive
P45S/Y219A
-
inactive
S392C
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
S442P
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
S469G
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
T467A
-
site-directed mutagenesis in the connection domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
Y219A
-
inactive
Y219D
-
inactive
Y219E
-
inactive
Y219S
-
inactive
Y299C
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
D39A
Saccharomyces cerevisiae W-303
-
inactive
-
Y219A
Saccharomyces cerevisiae W-303
-
inactive
-
Y219D
Saccharomyces cerevisiae W-303
-
inactive
-
Y219E
Saccharomyces cerevisiae W-303
-
inactive
-
Y219S
Saccharomyces cerevisiae W-303
-
inactive
-
D136H
Q8EE30
stabilization in melting temperature by 9.7 degrees and 6.1 kJ per mol. 65% odf wild-type activity
N29K/D39G/M76V/K90N
Q8EE30
stabilization in melting temperature by 18.7 degrees. 70% odf wild-type activity
N29K/D39G/M76V/K90N/R97G
Q8EE30
stabilization in melting temperature by 22.1 degrees. 65% of wild-type activity
N29K/D39G/M76V/K90N/R97G/D136H
Q8EE30
stabilization in melting temperature by 28.8 degrees. 43% of wild-type activity
R97G
Q8EE30
stabilization in melting temperature by 5.4 degrees and 3.5 kJ per mol. 99% of wild-type activity
C58A/C145A
-
site-directed mutagenesis
D125N
-
mutation results in loss of dsRNase activity but not RNase H activity
D76N
-
no RNase H activity is detected
D7N
-
site-directed mutagenesis
D7N
-
enzyme loses RNase H activity and dsRNase activity in the presence of MnCl2
DELTAG144-T149
-
mutant enzyme lacking the C-terminal tail. The unfolding transition of the wild-type enzyme occurs much later than the mutant enzyme at high temperature
E52Q
-
no RNase H activity is detected
R118A
-
the specific activities of R118A-RNase HI for both 12-bp RNA/DNA and RNA/RNA substrates are reduced by approximately 10fold as compared to those of the wild-type protein
D125N
Sulfolobus tokodaii 7
-
mutation results in loss of dsRNase activity but not RNase H activity
-
D76N
Sulfolobus tokodaii 7
-
no RNase H activity is detected
-
D7N
Sulfolobus tokodaii 7
-
enzyme loses RNase H activity and dsRNase activity in the presence of MnCl2
-
DELTAG144-T149
Sulfolobus tokodaii 7
-
mutant enzyme lacking the C-terminal tail. The unfolding transition of the wild-type enzyme occurs much later than the mutant enzyme at high temperature
-
E52Q
Sulfolobus tokodaii 7
-
no RNase H activity is detected
-
R118A
Sulfolobus tokodaii 7
-
the specific activities of R118A-RNase HI for both 12-bp RNA/DNA and RNA/RNA substrates are reduced by approximately 10fold as compared to those of the wild-type protein
-
D105A
-
site-directed mutagenesis, nearly inactive mutant
D135A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
D7A
-
site-directed mutagenesis, nearly inactive mutant
E8A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
D107N
-
site-directed mutagenesis, inactive mutant
R22A
-
site-directed mutagenesis, the R22A mutation does not alter Tm-RNase H2 activity on most substrates compared to the wild-type enzyme
W22A
Q9X122
site-directed mutagenesis, located in the hybrid binding domain
Y163F
-
site-directed mutagenesis, Y163 is a key residue involved in 2'-OH binding, and its mutation to phenylalanine seriously reduces activity against all tested substrates
A12S
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
A12S/K75M/A77P
-
site-directed mutagenesis, 40fold increased kcat/Km value compared to the wild-type enzyme, thermal stability similar to the wild-type enzyme
A77P
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
C13S/C63A/R135C
-
site-directed mutagenesis, 6.9% activity compared to the wild-type enzyme
C63A
-
site-directed mutagenesis, 94% activity compared to the wild-type enzyme
C63A/R135C
-
site-directed mutagenesis, 44% activity compared to the wild-type enzyme
D134H
-
site-directed mutagenesis, active site mutant, highly reduced catalytic activity
D134N
-
site-directed mutagenesis, active site mutant, similar to the wild-type enzyme
K75M
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
D22A
E0X765
inactive
D96A
E0X765
inactive
E23A
E0X765
inactive
N159A
E0X765
the mutant shows 20% and 2.6% activity in the presence of Mn2+ and Mg2+, respectively, compared to the wild type enzyme
N159D
E0X765
the mutant shows 17% and 5.0% activity in the presence of Mg2+ and Mn2+, respectively, compared to the wild type enzyme
L41A
O29634
no loss of activity
additional information
O29634
of the highly conserved residues, mutations at Ser38, Lys39, Leu41, Arg45, Ser139, and Asp167 do not significantly affect the enzyme activity. Conversion of Asp6 to Asn, Glu7 to Gln, or Asp101 to Asn almost completely inactivated the enzyme, suggesting that these carboxylic acid groups of D6, E7, and D101 are essential for catalysis
E188A
-
site-directed mutagenesis, crystal structure analysis of the mutant bound to divalent metal ions
additional information
-
Chlamydophila pneumoniae RNase HII can complement both Escherichia coli RNase HII and RNase HI, but Chlamydophila pneumoniae RNase HIII can only complement the latter
S94V
-
the mutation decreases the RNase H activity 3-6fold
additional information
Chlamydia pneumoniae AR39
-
Chlamydophila pneumoniae RNase HII can complement both Escherichia coli RNase HII and RNase HI, but Chlamydophila pneumoniae RNase HIII can only complement the latter
-
L56S
-
site-directed mutagenesis
additional information
-
construction of chimeric proteins of the Thermus thermophilus enzyme with the folding core of Chlorobium tepidum RNaseH, thermal stability analysis, overview
I25A
-
large destabilization, compared to wild-type. Mutant is active and retains a native-like fold. Mutation results in the equilibrium population of the folding intermediate under near-native conditions. The intermediate is undetectable in a series of heteronuclear single quantum coherences, revealing the dynamic nature of this partially unfolded form on the timescale of NMR detection
additional information
-
a Cys residue is substituted for Glu135 by site-directed mutagenesis in the mutant enzyme, in which all 3 free Cys residues are replaced by Ala and coupled with a maleimide group which is attached to the 5'-terminus of the nonadeoxyribonucleotide, 5'-GTCATCTCC-3', with a flexible tether. The resulting hybrid enzyme d9-C135/RNase H cleaves the phosphodiester bond between the fifth and sixth residues of the complementary nonaribonucleotide without addition of the oligodeoxyribonucleotide. The nonaribonucleotide is cleaved by the wild-type or unmodified mutant enzyme only when the complemetary oligoribonucleotide is present
additional information
-
a Cys residue is substituted for Glu135 by site-directed mutagenesis in the mutant enzyme, in which all 3 free Cys residues are replaced by Ala and coupled with a maleimide group which is attached to the 5'-terminus of the nonadeoxyribonucleotide, 5'-GTCATCTCC-3', with a flexible tether. The resulting hybrid enzyme d9-C135/RNase H shows site-specific cleavage of the 22-base RNA, 132-base RNA and 534-base RNA which contain a single target sequence, primarily at the unique phosphodiester bond within the target sequence. The hybrid enzyme performs multiple turnovers and at a substrate/enzyme ratio of 10:1 the RNAs are almost completely cleaved
additional information
-
all 3 Cys replaced with Ala, The recombinant enzyme is active and folds reversibly
additional information
-
construction of DNA-linked mutant enzyme, by cross-linking of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA, i.e. PPT-RNA, to the thiol group of Cys135 of the enzyme, mutant shows 4.2% activity compared to the wild-type enzyme
additional information
-
deletion of the basic loop in Escherichia coli RNase H inhibits but does not abolish activity. If the basic loop in Escherichia coli RNase H is inserted into an isolated inactive HIV-1 RNase H domain, Mn2+-dependent activity is partially restored
L52A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
additional information
-
construction of deletion mutants of RNase HIII by truncation of the N-domain, residues 1-79, the C-domain, residues 80-310, the RNase HIIIDELTAC domain, residues 1-299, and C-domainDELTAC, residues 80-299, the mutant show reduced activity, overview
additional information
-
construction of mutant proteins of the intact protein and isolated N-domain, in which six of the seventeen residues corresponding to those involved in DNA binding of TBP are individually mutated to Ala. All of the mutants exhibit decreased enzymatic activities and/or substrate-binding affinities when compared to those of the parent proteins
L60R
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
additional information
-
construction of deletion mutant H1[DELTA1-73]
additional information
-
full-length enzymes with defective HBDs indicates that this domain dramatically enhances both the specific activity and processivity of RNase H1
additional information
-
engineering of electrostatic and steric effects at the bottom of the minor groove for nuclease and thermodynamic stabilities and elicitation of RNase H, overview
additional information
-
knockdown of RNase H1, but neither of FEN1 nor DNA2, inhibits the recovery of mtDNA copy number
additional information
-
mapping of the positions of 29 mutations found in Aicardi-Goutieres syndrome patients, possible effects of these mutations on the protein stability and function, overview. Construction of deletion mutants AB14233C and ABDELTAPIPC, deletion mutant AB14-233C crystallizes more readily than the AB-PIPC and yields larger and regular crystals
Y29F
-
site-directed mutagenesis in the hybrid binding domain, the mutation abolishes dsRNA binding
additional information
Q8Y7K4
lmo1273 can complement an Escherichia coli rnhA-rnhB thermosensitive growth phenotype, suggesting that it encodes a functional RNase H. DELTAlmo1273: Chromosomal deletion mutant. Inactivation of lmo1273 provokes a strong attenuation of virulence in the mouse model, and kinetic studies in infected mice reveals that multiplication of the lmo1273 mutant in target organs is significantly impaired. DELTAlmo1272/DELTA1273 double mutant. MIC2067-lmo1273 using the Escherichia coli strain MIC2067 (an rnhA-rnhB double mutant strain) and transformed it with plasmid pTrc99A-lmo1273, carrying the lmo1273 gene under IPTG-inducible promoter control
G37S
Q9CWY8
mutation in subunit H2A identified in patients with Aicardi-Goutieres' syndrome. Mutation appears to distort the active site accounting for the demonstrated substrate specificity modification
additional information
P9WLH5
fusion protein of maltose binding protein and the N-terminal RNase H domain shows RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein has additional CobC activity
additional information
-
fusion protein of maltose binding protein and the N-terminal RNase H domain shows RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein has additional CobC activity
-
M520V
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
additional information
-
construction of several deletion mutants
additional information
-
generation of Ty1 reverse transcriptase/RNase H Mn2+ suppressor mutants capable of increased Ty1 transposition in pmr1DELTA cells for Mn2+ inhibition analysis, PMR1 codes for a P-type ATPase that regulates intracellular calcium and manganese ion homeostasis, and pmr1 mutants accumulate elevated intracellular manganese levels and display 100-fold less transposition than PMR1+ cells, suppressor point mutations localize not to the reverse transcriptase itself but to the RNase H domain of the protein, overview
E8Q
-
site-directed mutagenesis
additional information
-
the Sto-RNase HI C-terminal residues, -IGCIILT, are introduced as a tag on three proteins. Each chimeric protein is more stable than its wild-type protein
additional information
-
truncated mutant ST0519_1-195 retains only partial activity, while truncated mutant ST0519_1-196 completely loses its activity. Computational analysis of the substrate binding site through construction of diverse truncation mutants, overview
H132A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
additional information
-
construction of several truncation mutants, comprising residues 1-198, 1-203, 1-207, 1-213, or 1-217 of the wild-type enzyme, the truncated mutants' activities are increased or reduced compared to the wild-type enzyme, overview
G21S
-
site-directed mutagenesis, the mutation is located in the conserved GRG 2'-OH-sensing motif, the mutant has much lower activity on RNA/DNA and DNA-RNA/DNA in the presence of Mn2+. In the presence of Mg2+ it also shows reduced activity on substrates with (5')RNA-DNA(3') junction
additional information
-
construction of a truncated mutant with 15 residues removed from the C-terminus
additional information
Q9X122
the C-terminal RNase H domain loses the ability to suppress the RNase H deficiency of an Escherichia coli rnhA mutant. The substrate binding affinity of Tma-RNase HI is greatly reduced on removal of the hybrid binding domain or the mutation
L56S
-
site-directed mutagenesis
additional information
-
construction of DNA-linked mutant enzyme, by cross-linking of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA, i.e. PPT-RNA, to the thiol group of Cys13 or Cys135 of the enzyme, mutants shows 0.69% activity compared to the wild-type enzyme
additional information
-
isolation of a mutant enzyme with enhanced activity at moderate temperatures, genetic method development
additional information
-
populating the folded region of the intermediate mimic by protein engineering
additional information
-
construction of chimeric proteins of the Thermus thermophilus enzyme with the folding core of Chlorobium tepidum RNaseH, thermal stability analysis, overview
additional information
-
construction of several N-terminally truncated enzyme forms for investigation of structure-function relationship
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant I53 and L56 point mutants after being expressed insolubly in inclusion bodies in Escherichia coli
-
comparison of the folding trajectories of the three-state RNase H mutant D10A and the two-state RNase H mutant D10A/I53D, proteins with the same native-state topology but altered regional stability. Both versions of RNase H fold through a similar trajectory with similar high-energy conformations. Mutations in the core and the periphery of the protein affect similar aspects of folding for both variants
-
refolding from purified urea-denatured form with low yield
-
study on thermal and mechanical folding and unfolding mechanisms. Mechanical and thermal unfolding proceed through three stable states that are similar. The one difference between the two regimes is in the transition occurring at the most denaturing conditions. For the thermal case, both secondary and tertiary structures melt. For the mechanical case, the secondary structure of the helices remains largely intact, while the bundle itself unfolds. Of the major secondary structure motifs, alpha-helices are more stable than beta-sheets
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
hybrid RNase H molecules with various oligodeoxyribonucleotides may facilitate structural studies of RNA and prove useful as tool for RNA manipulations
analysis
-
facile method that identifies single-stranded regions in RNA using short, randomized DNA oligonucleotides and RNase H cleavage. These regions are then used as constraints in secondary structure prediction. This method was used to improve the secondary structure prediction of Escherichia coli 5S rRNA. The addition of constraints from RNase H cleavage improves the prediction to 100% of base pairs. The same method was used to generate secondary structure constraints for yeast tRNAPhe, which is accurately predicted in the absence of constraints to 95%. The method is advantageous over other single-stranded nucleases since RNase H is functional in physiological conditions and can be used for any RNA to identify accessible binding sites for oligonucleotides or small molecules
analysis
-
quadruplex-based fluorescence assay for sensitive, facile, real-time, and label-free detection of RNase H activity and inhibition by using a G-quadruplex formation strategy. A RNA-DNA substrate is prepared, with the DNA strand designed as a quadruplex-forming oligomer. Upon cleavage of the RNA strand by RNase H, the released G-rich DNA strand folds into a quadruplex in the presence of monovalent ions and interacts with a specific G-quadruplex binder, N-methyl mesoporphyrin IX, giving a dramatic increase in fluorescence and serving as a reporter of the reaction. The assay is simple in design, fast in operation and convenient
molecular biology
-
the enzyme can be useful in regulation of RNA degradation in applications of technologies involving mRNA, method development, overview
pharmacology
Q8WR57
the enzyme is a potential target for antileishmanial chemotherapy
pharmacology
Q8WSZ0
the enzyme is a potential target for antileishmanial chemotherapy