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Information on EC 3.1.26.4 - ribonuclease H and Organism(s) Thermotoga maritima and UniProt Accession Q9X017

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.26 Endoribonucleases producing 5'-phosphomonoesters
                3.1.26.4 ribonuclease H
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This record set is specific for:
Thermotoga maritima
UNIPROT: Q9X017 not found.
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The taxonomic range for the selected organisms is: Thermotoga maritima
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Endonucleolytic cleavage to a 5'-phosphomonoester
Synonyms
reverse transcriptase, ribonuclease h, rnase h2, rnase hii, rnaseh2a, rnaseh1, ribonuclease hi, ribonuclease h2, rnase hiii, ribonuclease h1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
type 2 RNase H
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endoribonuclease H
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hybrid nuclease
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hybrid ribonuclease
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hybridase
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hybridase (ribonuclease H)
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nuclease, hybrid ribo-
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nuclease, ribo-, H
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-
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P32
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ribonuclease H
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ribonuclease H I
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RNA*DNA hybrid ribonucleotidohydrolase
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-
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RNase H
RNase H1
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-
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RNase HI
RNase HII
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-
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RNase HIII
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
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-
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CAS REGISTRY NUMBER
COMMENTARY hide
9050-76-4
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
?
DNA-RNA-DNA/DNA hybrid + H2O
?
show the reaction diagram
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
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-
?
poly(rA)/poly(dT) + H2O
?
show the reaction diagram
-
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
an RNA/DNA hybrid (RNA12/DNA12)
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-
?
D13-R4-D12-D29 hybrid + H2O
?
show the reaction diagram
-
-
-
?
M13 DNA/RNA hybrid + H2O
?
show the reaction diagram
-
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
-
-
-
?
additional information
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
show the reaction diagram
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00039
M13 DNA/RNA hybrid
wild-type enzyme, pH 9.0, 30°C, in presence of 50 mM KCl
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.48
substrate M13 DNA/RNA hybrid, enzyme mutant W22A, pH 9.0, 30°C, in presence of 50 mM KCl
3.6
substrate M13 DNA/RNA hybrid, wild-type enzyme, pH 9.0, 30°C, in presence of 50 mM KCl
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 10
Mg-dependent hydrolysis activity by Tm-RNase H2 gradually increases from pH 7.5 to 10 without reaching a maximum
8.5
Mn-dependent activity of Tm-RNase H2 is the highest at around pH 8.5
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 10
activity range dependent on cation added
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
26630
1 * 26630, SDS-PAGE
27000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 26630, SDS-PAGE
additional information
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D107N
site-directed mutagenesis, inactive mutant
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
R22A
site-directed mutagenesis, the R22A mutation does not alter Tm-RNase H2 activity on most substrates compared to the wild-type enzyme
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
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
66.1
melting temperature
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the C-terminal extension of the enzyme functions as a substrate-binding domain and stabilizes the RNase H domain
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HiTrap Q column chromatography, HiTrap heparin column chromatography, and Superdex 200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli MIC2067(DE3) cells
expression of wild-type and truncated D107N mutant enzymes in Escherichia coli
overproduced in Escherichia coli
RNase HI sequence comparisons, expression of wild-type and mutant enzymes in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Jongruja, N.; You, D.J.; Kanaya, E.; Koga, Y.; Takano, K.; Kanaya, S.
The N-terminal hybrid binding domain of RNase HI from Thermotoga maritima is important for substrate binding and Mg2+-dependent activity
FEBS J.
277
4474-4489
2010
Thermotoga maritima (Q9X122)
Manually annotated by BRENDA team
Rychlik, M.P.; Chon, H.; Cerritelli, S.M.; Klimek, P.; Crouch, R.J.; Nowotny, M.
Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage
Mol. Cell
40
658-670
2010
Thermotoga maritima (Q9X017)
Manually annotated by BRENDA team
Permanasari, E.D.; Angkawidjaja, C.; Koga, Y.; Kanaya, S.
Role of N-terminal extension of Bacillus stearothermophilus RNase H2 and C-terminal extension of Thermotoga maritima RNase H2
FEBS J.
280
5065-5079
2013
Geobacillus stearothermophilus, Thermotoga maritima (Q9X017), Thermotoga maritima DSM 3109 (Q9X017)
Manually annotated by BRENDA team
Jongruja, N.; You, D.; Kanaya, E.; Koga, Y.; Takano, K.; Kanaya, S.
The N-terminal hybrid binding domain of RNase HI from Thermotoga maritima is important for substrate binding and Mg2+-dependent activity
FEBS J.
277
4474-4489
2010
Thermotoga maritima (Q9X122), Thermotoga maritima DSM 3109 (Q9X122)
Manually annotated by BRENDA team