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Information on EC 3.1.26.4 - ribonuclease H and Organism(s) Thermus thermophilus and UniProt Accession P29253
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3.1.26.4 ribonuclease HSpecify your search results
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- 3.1.26.4
-
antiretroviral
- nucleoside
- viruses
-
nnrti
-
virological
-
hiv-infected
-
nonnucleoside
- leukemia
- subtype
-
integrase
- lymphocyte
- strand
- cd4
- efavirenz
-
retroviral
- zidovudine
-
drug-resistant
- infectious
- nevirapine
- retroviruses
- telomerase
- nucleic
- tenofovir
- lamivudine
-
anti-hiv
-
first-line
- virion
- t-cells
-
surveillance
-
retrotransposons
-
haart
- polymerases
-
proviral
-
swab
- covid-19
- coronavirus
- ritonavir
- sars-cov-2
-
outbreak
-
telomeric
-
nucleocapsid
-
rna-dependent
-
resistance-associated
- dntp
-
treatment-naive
-
hiv-positive
-
moloney
- viremia
-
cross-resistance
- pharmacology
- drug development
- analysis
-
once-daily
- molecular biology
The taxonomic range for the selected organisms is: Thermus thermophilus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
reverse transcriptase, ribonuclease h, rnase h2, rnase hii, rnaseh2a, rnaseh1, ribonuclease hi, ribonuclease h2, rnase hiii, ribonuclease h1, 
more
topSYNONYM 
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
-
-
-
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RNase H
RNase H1
-
-
-
-
RNase HI
RNase HII
-
-
-
-
RNase HIII
-
-
-
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hybrid nuclease
-
-
-
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hybrid ribonuclease
-
-
-
-
hybridase
-
-
-
-
hybridase (ribonuclease H)
-
-
-
-
ribonuclease H
-
-
-
-
RNase H
-
-
-
-
RNase HI
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Endonucleolytic cleavage to a 5'-phosphomonoester
active site residues are Asp10, Gu48, Asp70, His124, Asp134
-
Endonucleolytic cleavage to a 5'-phosphomonoester
evolutionary conserved flexible regions are important for catalysis, structure function relationship, enthalpic/entropic compensation mechanism, overview
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
hydrolysis of phosphoric ester
-
-
-
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CAS REGISTRY NUMBER
COMMENTARY
9050-76-4
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
DNA-RNA-DNA hybrid + H2O
?
-
specific hydrolysis of the RNA strand of the hybrid
-
-
?
PPT-RNA + H2O
?
-
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-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
M13 DNA/RNA hybrid
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0011
DNA-RNA-DNA hybrid
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mutant A12S/K75M and A12S/K75M/A77P, pH 8.0, 30°C
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additional information
additional information
-
thermodynamics of wild-type and mutant enzymes
-
additional information
additional information
-
thermodynamics, heat capacity measurement, thermal stability and flexibility of the enzyme
-
additional information
additional information
-
thermodynamic analyses of mutant enzymes, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
activity of wild-type and mutant enzymes at different temperatures
additional information
-
activity of wild-type and mutant enzymes, determination by spectrophotometric assay, at different temperatures
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
65
-
wild-type enzyme, assay at, substrate PPT-RNA, DNA-C135-linked mutant enzyme shows optimal activity with this substrate at 65°C
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
enzyme is composed of five alpha-helices (A to E) and five beta-strands (I to V). The intermediate mimic is a monomer
additional information
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
-
three-dimensional structure of wild-type enzyme
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A12S
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random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
A12S/K75M/A77P
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site-directed mutagenesis, 40fold increased kcat/Km value compared to the wild-type enzyme, thermal stability similar to the wild-type enzyme
A77P
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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
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site-directed mutagenesis, 94% activity compared to the wild-type enzyme
C63A/R135C
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site-directed mutagenesis, 44% activity compared to the wild-type enzyme
D134H
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site-directed mutagenesis, active site mutant, highly reduced catalytic activity
D134N
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site-directed mutagenesis, active site mutant, similar to the wild-type enzyme
K75M
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random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
additional information
additional information
populating the folded region of the intermediate mimic by protein engineering
additional information
-
populating the folded region of the intermediate mimic by protein engineering
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
-
construction of chimeric proteins of the Thermus thermophilus enzyme with the folding core of Chlorobium tepidum RNaseH, thermal stability analysis, overview
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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 75°C
82.1
-
melting temperature in presence of 1.2 M guanidinium hydrochloride
90
additional information
additional information
-
melting temperature is 86°C, conserved quantitative stability/flexibility relationships, QSFR, thermodynamics, thermal stability and flexibility of the enzyme
additional information
-
analysis of thermal unfolding, the folding core of Thermus thermophilus RNaseH plays an important role in the unfolded state of this protein
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant recombinant chimeric mutant enzyme from Escherichia coli strain BL21(DE3) by heparin affinity chromatography, and His-tagged mutant L56S by nickel affinitychromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of recombinant chimeric mutant enzyme and of His-tagged mutant L56S in Escherichia coli strain BL21(DE3)
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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
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overexpression of wild-type and mutant enzymes in Escherichia coli strain HB101
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kanaya, S.; Itaya, M.
Expression, purification, and characterization of a recombinant ribonuclease H from Thermus thermophilus HB8
J. Biol. Chem.
267
10184-10192
1992
Escherichia coli, Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Hirano, N.; Haruki, M.; Morikawa, M.; Kanaya, S.
Enhancement of the enzymatic activity of ribonuclease HI from Thermus thermophilus HB8 with a suppressor mutation method
Biochemistry
39
13285-13294
2000
Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Gromiha, M.M.
Factors influencing the stability of alpha-helices and beta-strands in thermophilic ribonuclease H
Prep. Biochem. Biotechnol.
31
103-112
2001
Thermus thermophilus
Haruki, M.; Nogawa, T.; Hirano, N.; Chon, H.; Tsunaka, Y.; Morikawa, M.; Kanaya, S.
Efficient cleavage of RNA at high temperatures by a thermostable DNA-linked ribonuclease H
Protein Eng.
13
881-886
2000
Escherichia coli, Thermus thermophilus
Livesay, D.R.; Jacobs, D.J.
Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
Proteins
62
130-143
2006
Escherichia coli, Thermus thermophilus
Zhou, Z.; Feng, H.; Ghirlando, R.; Bai, Y.
The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H
J. Mol. Biol.
384
531-539
2008
Thermus thermophilus (P29253), Thermus thermophilus
Ratcliff, K.; Marqusee, S.
Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues
Biochemistry
49
5167-5175
2010
Chlorobaculum tepidum, Thermus thermophilus
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