Information on EC 3.1.13.2 - exoribonuclease H

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.1.13.2
-
RECOMMENDED NAME
GeneOntology No.
exoribonuclease H
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY hide
9050-76-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Avian sarcoma leukosis virus
-
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
MSV-MLV(H)
-
-
Manually annotated by BRENDA team
HBV
-
-
Manually annotated by BRENDA team
Herpes simplex virus
HSV
-
-
Manually annotated by BRENDA team
Herpes simplex virus HSV
HSV
-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
HXB2 strain
-
-
Manually annotated by BRENDA team
Rauscher leukemia virus
RD-feline leukemia virus
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
RAV-1
-
-
Manually annotated by BRENDA team
i.e. SIVCPZ
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
12 bp RNA/DNA hybrid + H2O
?
show the reaction diagram
18mer DNA-RNA hybrid + H2O
?
show the reaction diagram
-
the RNA is labeled with 6-carboxytetramethyl rhodamine at the 3' end and annealed to complementary nonlabeled DNA
-
-
?
3' end-labeled 41-nt RNA annealed to a 77-nt DNA template
DNA + RNA fragments
show the reaction diagram
-
-
the most RNA fragments are cleaved by a combination of primary, secondary primary, and 5-nt cuts
?
5' end-labeled 41-nt RNA annealed to a 77-nt DNA template
DNA + RNA fragments
show the reaction diagram
-
-
The first product observed is the primary cut. The primary cut occurs faster than the secondary cut
?
5' end-labeled 50-nt RNA annealed to a 77-nt DNA template
DNA + RNA fragments
show the reaction diagram
-
-
The first product observed is the primary cut. The primary cut occurs faster than the secondary cut
?
5' end-labeled RNA
RNA fragments
show the reaction diagram
-
cleavage of 267 nt RNA substrate to produce a 47 nt long product, the second cleavage produces RNA fragments that are 38 nt long
-
?
5' RNA-DNA duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
show the reaction diagram
-
-
-
?
5'-end-labeled RNA
RNA fragments
show the reaction diagram
5'-fluorescein-labeled RNA/DNA hybrid + H2O
?
show the reaction diagram
CGK1 + H2O
?
show the reaction diagram
-
RNase H substrate CGK1 is obtained by annealing 5'-cap-labelled R1 5'-m7Gppp*GmAAUACUCAAGCUAUGCAUC-3' with DNA oligonucleotide D1. The RNA oligonucleotide is blocked at the 5' end by adding a guanosyl-5'-5'-guanosine triphosphate cap structure
-
-
?
DNA-DNA hybrid duplex + H2O
?
show the reaction diagram
DNA-RNA duplex + H2O
?
show the reaction diagram
DNA-RNA hybrid + H2O
?
show the reaction diagram
DNA-RNA hybrid + H2O
DNA + RNA nucleotides
show the reaction diagram
-
-
-
?
DNA-RNA hybrid + H2O
DNA nucleotides + RNA nucleotides
show the reaction diagram
-
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
show the reaction diagram
DNA/DNA + H2O
?
show the reaction diagram
double-stranded RNA + H2O
?
show the reaction diagram
HTS-1 RNA-DNA + H2O
?
show the reaction diagram
HTS-2 RNA-DNA + H2O
?
show the reaction diagram
poly(rA)n-poly(dT)n
?
show the reaction diagram
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
show the reaction diagram
-
poly(rGdC)
-
-
?
RNA/DNA hybrid + H2O
?
show the reaction diagram
single-stranded RNA + H2O
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
12 bp RNA/DNA hybrid + H2O
?
show the reaction diagram
DNA-RNA hybrid + H2O
?
show the reaction diagram
DNA-RNA hybrid + H2O
DNA + RNA nucleotides
show the reaction diagram
P03366
-
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
show the reaction diagram
double-stranded RNA + H2O
?
show the reaction diagram
RNA/DNA hybrid + H2O
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
10 mM Co2+ supports catalytic activity
Na+
LC11-RNase H1 exhibits the highest activity in the presence of 10 mM NaCl. Its activity gradually decreases as the salt concentration increases
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-1,9,14-trioxo-6,7,9,14-tetrahydrotetraceno[1,2-g]phthalazin-2(1H)-yl)acetic acid
-
-
(2E)-2-[(4-chlorophenyl)hydrazono]propanoic acid
-
4-chlorophenylhydrazone of pyruvic acid, shows poor inhibitory activity against HIV-1 RNase H because of the storage of one or two carboxylic acid moieties
(2Z)-2-hydroxy-4-oxopent-2-enoic acid
-
-
(E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide
i.e. DHBNH, highly specific, noncompetitive, binding site analysis, the inhibitor binds near both the polymerase active site and the non-nucleoside reverse transcriptase inhibitor binding pocket, it specifically interacts with conserved residues Asp186 and Trp229 and has substantial interactions with the backbones of several less well-conserved residues, overview, substituted inhibitor derivatives, that interact with the nucleoside analog RT inhibitor-binding pocket, inhibit both the polymerase and RNH activities of reverse transcriptase, DHBNH interacts with other residues, including Val108, Leu187, Tyr188, Lys223, Phe227, and Leu228
1,3,4,5-tetragalloylapiitol
1,4-Naphthoquinone
-
-
1,9,11,14-tetrahydroxy-3-[(E)-{[(2-hydroxyphenyl)carbonyl]hydrazono}methyl]-7-methoxy-10-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
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-
1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-3-[(E)-{[(4-methylphenyl)sulfonyl]hydrazono}methyl]-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-3-{(E)-[(4-nitrophenyl)hydrazono]methyl}-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-8,13-dioxo-3-(1,2,3,4-tetrahydroquinazolin-2-yl)-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-8,13-dioxo-3-[(E)-(tetracyclo[5.3.1.03,9.05,9]undec-1-ylimino)methyl]-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-8,13-dioxo-3-{(E)-[(phenylcarbonyl)hydrazono]methyl}-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2,3-dicarboxylic acid
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1,9,11,14-tetrahydroxy-7-methoxy-3-[(E)-(methoxyimino)methyl]-10-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
1-(4-chlorophenyl)-2-(1-methylethylidene)hydrazine
-
4-chlorophenylhydrazone of acetone, shows poor inhibitory activity against HIV-1 RNase H because of the storage of one or two carboxylic acid moieties
10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-1,9,14-trioxo-6,7,9,14-tetrahydrotetraceno[1,2-g]phthalazine-2(1H)-carboximidamide
-
-
10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-2,3,4,4a,6,7-hexahydropyrimido[2,1-a]tetraceno[1,2-f]isoindole-9,14,17(1H)-trione
-
-
10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-2-phenyl-6,7-dihydrotetraceno[1,2-g]phthalazine-1,9,14(2H)-trione
-
-
10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-2-propyl-6,7-dihydrotetraceno[1,2-g]phthalazine-1,9,14(2H)-trione
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-
10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-6,7-dihydrotetraceno[1,2-g]phthalazine-1,9,14(2H)-trione
-
-
12,14,17,18-tetrahydroxy-10-methoxy-13-methyl-6,6a,8,9-tetrahydrotetraceno[1',2':5,6]isoindolo[2,1-a]quinazoline-11,16,19(5H)-trione
-
-
15,16-dihydroxy-8-methoxy-12-[(methoxycarbonyl)oxy]-11-methyl-1,9,14-trioxo-2-propyl-1,2,6,7,9,14-hexahydrotetraceno[1,2-g]phthalazin-10-yl acetate
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-
2'-deoxy-4'-ethyl-3,4-dihydrothymidine
-
-
2'-deoxy-4'-ethynyl-2-fluoroadenosine
-
-
2'-deoxy-4'-methyl-3,4-dihydrothymidine
-
-
2,4,17,18-tetrahydroxy-6-methoxy-3-methyl-7,9b-dihydrotetraceno[1',2':5,6]isoindolo[1,2-b][1,3]benzothiazole-5,16,19(8H)-trione
-
-
2,7-dihydroxy-4-isopropylcyclohepta-2,4,6-trienone
2,7-dihydroxyisoquinoline-1,3(2H,4H)-dione
-
-
2-(10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-1,9,14-trioxo-6,7,9,14-tetrahydrotetraceno[1,2-g]phthalazin-2(1H)-yl)ethyl acetate
-
-
2-(4-fluorophenyl)-N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)acetamide
-
-
2-amino-12-ethyl-7-(1-hydroxypropyl)-8-methylindolizino[1,2-b]quinolin-9(11H)-one
-
mappicine analogue
2-amino-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophene-3-carboxamide
2-aminoisoquinoline-1,3(2H,4H)-dione
-
-
2-chloro-7-(2-cyclohexyl-1-hydroxyethyl)-8-methyl-12-propylindolizino[1,2-b]quinolin-9(11H)-one
-
mappicine analogue
2-hydroxy-4H-isoquinoline-1,3-dione
-
specific inhibition of isolated RNase H domain and of the full length reverse transcriptase, IC50 value for the isolated RNase H domain is 0.00043 mM
2-hydroxy-6-pentadecylbenzoic acid
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
2-hydroxy-6-[(8Z)-pentadec-8-en-1-yl]benzoic acid
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
2-hydroxy-7-(4-hydroxyphenyl)isoquinoline-1,3(2H,4H)-dione
-
-
2-hydroxy-7-iodoisoquinoline-1,3(2H,4H)-dione
-
-
2-hydroxy-7-nitroisoquinoline-1,3(2H,4H)-dione
-
-
2-hydroxy-7-phenylisoquinoline-1,3(2H,4H)-dione
-
-
2-hydroxy-7-[4-(trifluoromethyl)phenyl]isoquinoline-1,3(2H,4H)-dione
-
-
2-hydroxyisoquinoline-1,3(2H,4H)-dione
2-methoxyisoquinoline-1,3(2H,4H)-dione
-
-
2-[(10Z)-heptadec-10-en-1-yl]-6-hydroxybenzoic acid
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
3'-azido-3'-deoxythymidine
3'-azido-3'-deoxythymidine 5'-(dihydrogen phosphate)
-
inhibits RNase H in vitro, but is not selectively active against RNase H. Does not exhibit inhibitory activity against RNase H in the HIV-1 replication process
3'-azido-3'-deoxythymidine 5'-phosphate
-
more sensitive to inhibition with poly(rGdC) than with poly(rAdT) as substrate. Competitive inhibitor with respect to substrate in Mn2+, uncompetitive inhibitor in Mg2+
3,4-dihydroxy-N'-[(E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
-
specific inhibitor of reverse transcriptase RNase H activity (IC50 value is about 0.5 microM) and has relatively limited activity against the DNA polymerase activity of reverse transcriptase. It is non-cytotoxic and inhibits the replication of a variety of drug-resistant HIV-1 reverse transcriptase mutants
3,7-dihydroxytropolones
-
-
3,9,11,14,15-pentahydroxy-7-methoxy-N,N,N,10-tetramethyl-1,8,13-trioxo-1,3,5,6,8,13-hexahydro-2H-tetraceno[1,2-f]isoindol-2-aminium
-
-
3-pentadecylphenol
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
3-tridecylphenol
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
3-[(10Z)-heptadec-10-en-1-yl]phenol
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
3-[(8Z)-pentadec-8-en-1-yl]phenol
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
3-[(E)-(carbamimidoylhydrazono)methyl]-1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
3-[(E)-(tert-butylhydrazono)methyl]-1,9,11,14-tetrahydroxy-7-methoxy-10-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxylic acid
-
-
3-[(E)-[4-[(E)-2-carboxyethenyl]phenyl]diazenyl]-7-[([6-[(E)-[4-[(E)-2-carboxyethenyl]phenyl]diazenyl]-5-hydroxy-7-sulfonatonaphthalen-2-yl]carbamoyl)amino]-4-hydroxynaphthalene-2-sulfonate
-
-
4'-chloro-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide
-
4-(1-chloro-1,1-difluoromethyl)-4-(2-phenylethynyl)-6-chloro-2H-3,1-benzoxazin-2-one
-
i.e. NNRTI, an efavirenz analogue, IC50 values for wild-type enzyme are 0.000002-0.000005 mM with substrates DNA-17-nucleotide-RNA hybrid or DNA-18-nucleotide-RNA hybrid, and 0.001 mm for substrate DNA-15-nucleotide-RNA hybrid or DNA-16-nucleotide-RNA hybrid, effect on mutant enzymes, overview
4-(10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-1,9,14-trioxo-6,7,9,14-tetrahydrotetraceno[1,2-g]phthalazin-2(1H)-yl)benzoic acid
-
-
4-(5-benzamidothiophen-2-yl)-2,4-dioxobutanoic acid
-
IC50 values determined by two different assay variants
4-(dimethylamino)-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
-
4-methoxy-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
-
4-tert-butyl-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
-
4-[(4'-aminomethyl-1,1'-biphenyl)methyl]-1-hydroxy-1,8-naphthyridin-2-one
4-[1-(4-fluorobenzyl)-1H-pyrrol-2-yl]-2,4-dioxobutanoic acid
-
L-731,988
4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid
-
a diketo acid RNase H inhibitor, IC50 values for wild-type and mutant enzymes are 0.002-0.0035 mM with all substrates, effect on mutant enzymes, overview
4-[5-(benzoylamino)tien-2-yl]-2,4-dioxobutanoic acid
-
diketo acid derivative
4-[5-benzoylamino) thien-2-yl]-2,4-dioxobutanoic acid
-
inhibits RNase H by binding to the active site and chelating the essential Mg2+
5-chloro-2-hydroxyisoquinoline-1,3(2H,4H)-dione
-
-
5-chloro-2-hydroxyisoquinoline-1,3(2H,4H-dione)
-
is not candidate therapeutics because it is cytotoxic
5-nitrofuran-2-carboxylic acid adamantan-1-carbamoyl methyl ester
5-nitrofuran-2-carboxylic acid [[4-(4-bromophenyl)-thiazol-2-yl]-(tetrahydro-furan-2-yl-methyl)-carbamoyl] methyl ester
-
20-25 microM effectively inhibited HIV-1 replication
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 inhibited HIV-1 replication
5-tridecylbenzene-1,3-diol
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
5-[(8Z)-pentadec-8-en-1-yl]benzene-1,3-diol
-
isolated from the CH2Cl2 extracts of the sacrotestas of Ginkgo biloba
7-(3,4-dihydroxyphenyl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione
-
-
7-(4-fluorophenyl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione
-
-
7-(furan-2-yl)-2-hydroxy-isoquinoline-1,3(2H,4H)-dione
7-bromo-2-hydroxyisoquinoline-1,3(2H,4H)-dione
-
-
7-chloro-2-hydroxyisoquinoline-1,3(2H,4H)-dione
-
-
8-methoxy-11-methyl-1,9,14-trioxo-2-phenyl-1,2,6,7,9,14-hexahydrotetraceno[1,2-g]phthalazine-10,12,15,16-tetrayl tetraacetate
-
-
8-methoxy-11-methyl-1,9,14-trioxo-2-propyl-1,2,6,7,9,14-hexahydrotetraceno[1,2-g]phthalazine-10,12,15,16-tetrayl tetraacetate
-
-
9,11,14,15-tetrahydroxy-7-methoxy-10-methyl-8,13,16-trioxo-1,2,3a,5,6,8,13,16-octahydrotetraceno[1,2-f][1,3]thiazolo[2,3-a]isoindole-1-carboxylic acid
-
-
acetylshikonin
-
inhibits weakly
alpha-thujaplicin
ardimerin digallate
beta-thujaplicin
beta-thujaplicinol
BPH218
-
potent inhibitor of ATP-mediated phosphorolytic excision of 3'-terminal zidovudine 5'-monophosphate (in vitro IC50 value is about 2 microM)
capravirine
-
a nonnucleoside reverse transcriptase inhibitor, inhibits the 5' to 3' directed RNase H activity
Cl-
-
the wild-type and mutant enzymes bind the substrate considerably less tightly at higher concentrations
deoxyshikonin
-
inhibits weakly
Dextran sulfate
-
inhibits RNase H in vitro, but is not selectively active against RNase H. Does not exhibit inhibitory activity against RNase H in the HIV-1 replication process
-
dihydroxy benzoyl naphthyl hydrazone
-
also have inhibitory activity against drug-resistant HIV-1 RT variants Y181C RT and Y188l RT. NNRTI Efavirenz shows no inhibitory effect under the same conditions
efavirenz
ethyl (5E)-6-[1-(4-fluorobenzyl)-1H-pyrrol-2-yl]-2,4-dioxohex-5-enoate
-
RDS 1643, good selectivity and high potency in enzyme and cell culture assay
ethyl 3-(10,12,15,16-tetrahydroxy-8-methoxy-11-methyl-1,9,14-trioxo-6,7,9,14-tetrahydrotetraceno[1,2-g]phthalazin-2(1H)-yl)propanoate
-
-
gamma-thujaplicin
GW8248
-
a nonnucleoside reverse transcriptase inhibitor, inhibits the 5' to 3' directed RNase H activity
heparin
-
inhibits RNase H in vitro, but is not selectively active against RNase H. Does not exhibit inhibitory activity against RNase H in the HIV-1 replication process
hyemaloside A
-
isolated from the evergreen tree Eugenia hyemalis
hyemaloside B
-
isolated from the evergreen tree Eugenia hyemalis
hyemaloside C
-
isolated from the evergreen tree Eugenia hyemalis
illimaquinone
juglone
-
poor inhibitory activity
madurahydroxylactone
-
a secondary metabolite from the soil bacterium Nonomuraea rubra, belonging to the family of benzo[a]naphthacenequinone antibiotics
manicol
methyl 10,15,16-trihydroxy-8-methoxy-11-methyl-1,9,14-trioxo-2-phenyl-1,2,6,7,9,14-hexahydrotetraceno[1,2-g]phthalazin-12-yl carbonate
-
-
Mg2+
-
inhibitory at concentrations greater than 10 mM
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-methylbenzohydrazide
-
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-phenoxybenzohydrazide
-
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
-
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide
-
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)-2-phenylacetamide
-
-
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)-3-nitrobenzamide
-
-
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)-4-fluorobenzamide
-
-
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)acetamide
-
-
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)benzamide
-
-
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)pentanamide
-
-
N-(4-tert-butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone
N-(4-tert-butylbenzoyl)-2-hydroxynaphthaldehyde hydrazone
-
BBNH, the residue Tyr501 is integral in the binding interaction, mechanism
N-acyl hydrazone analogues
-
-
N-[3-(aminocarbonyl)-4,5-dimethyl-2-thienyl]-2-furancarboxamide
naphthazarin
-
inhibits weakly
nevirapine
non-nucleoside reverse transcriptase inhibitors
-
non-nucleotide or non-nucleoside reverse transcriptase inhibitor
-
nonnucleoside reverse transcriptase inhibitor
-
NNRTI
-
nootkatin
-
i.e. 2-hydroxy-5-(3-methyl-2-butenyl)-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
nucleoside analog reverse transcriptase inhibitor
-
NRTI
-
nucleoside analog RT inhibitors
-
nucleotide or nucleoside reverse transcriptase inhibitor
-
p-hydroxymercuribenzoate
Herpes simplex virus
-
5 mM lead to 90% inhibition
Phosphonoformate
-
the inhibitor that bind in the reverse transcriptase polymerase domain inhibits also RNase H activity, IC value for the wild-type enzyme is 0.0015 mM versus substrate DNA-18-nucleotide-RNA hybrid, with the other substrates the IC50 value is above 0.025 mM
Phosphonoformic acid
-
inhibits both the polymerase and the RNase H activities
Plumbagin
-
poor inhibitory activity
RNA-DNA duplex with bound drugs
-
two chimeric RNA-DNA duplexes mimicking intermediates of the reverse trancriptase reaction with bound 4,5-disubstituted 2-deoxystreptamine aminoglycosides, i.e. neomycin, paromomycin, and ribostamycin, inhibit specifically and competitively the RNase H cleavage reaction by 60-95% and 15-91%, respectively, overview
-
shikometabolin C
-
inhibits weakly
shikometabolin D
-
inhibits weakly
shikonin
-
inhibits weakly
single-stranded DNA aptamer RT1t49
-
single-stranded RNA aptamer RT1t49
-
tert-butyl [7-(1-hydroxypropyl)-8-methyl-9-oxo-12-(trimethylsilyl)-9,11-dihydroindolizino[1,2-b]quinolin-2-yl]carbamate
-
mappicine analogue
TMC-125
-
a nonnucleoside reverse transcriptase inhibitor, inhibits the 5' to 3' directed RNase H activity
trihydroxybenzoylbiphenyl carboxylate hydrazone
trihydroxybenzoylnaphthyl hydrazone
tropolone
zidovudine triphosphate
-
i.e. AZTTP
[(4-chlorophenyl) hydrazono] propanedioic acid
-
inhibits the RNase H of HIV-1 reverse transcriptase with potency similar to that of N-(4-tert-butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone. It is specific for RNase H and does not inhibit the DNA polymerase activity of reverse transcriptase. Inhibits RNase H by binding to the active site and chelating the essential Mg2+
[(4-chlorophenyl)hydrazono]propanedioic acid
-
inhibits by directly chelating Mg2+
[10,12,15,16-tetrakis(cyclohexyloxy)-8-methoxy-11-methyl-1,9,14-trioxo-6,7,9,14-tetrahydrotetraceno[1,2-g]phthalazin-2(1H)-yl]acetic acid
-
-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
AMP
-
activates, causes conformational changes on some sites of the enzyme N-terminus near strand beta2 and beta3 andhelix alphaA, residues 28-69
KCl
-
maximal enzyme activity at 0-20 mM
oligodeoxynucleotide
-
activation resulting in self-destruction of the virions
-
Stimulatory protein
-
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0000096
18mer DNA-RNA hybrid
-
pH 8.0, 37C, recombinant enzyme
-
0.000053
DNA-15-nucleotide-RNA hybrid
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.000052
DNA-16-nucleotide-RNA hybrid
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.000007
DNA-17-nucleotide-RNA hybrid
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.000011
DNA-18-nucleotide-RNA hybrid
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.000097 - 0.000106
DNA-RNA hybrid
-
0.003 - 0.066
poly(rA)n-poly(dT)n
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0135
DNA-15-nucleotide-RNA hybrid
Human immunodeficiency virus 1
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.017
DNA-16-nucleotide-RNA hybrid
Human immunodeficiency virus 1
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.0018
DNA-17-nucleotide-RNA hybrid
Human immunodeficiency virus 1
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.0032
DNA-18-nucleotide-RNA hybrid
Human immunodeficiency virus 1
-
pH 7.8, 37C, recombinant wild-type enzyme
-
0.025 - 3.5
DNA-RNA hybrid
-
0.0024 - 0.0034
poly(rA)n-poly(dT)n
-
0.0024
poly(rA)n-poly(dT)ne
Human immunodeficiency virus 1
-
mutant p66C280P/p51
-
additional information
additional information
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
240 - 36000
DNA-RNA hybrid
11646
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0043 - 0.0206
N-(4-tert-butylbenzoyl)-2-hydroxynaphthaldehyde hydrazone
additional information
additional information
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0005
(E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide
Human immunodeficiency virus 1
P03366
-
0.00013 - 0.00024
1,3,4,5-tetragalloylapiitol
0.0095
1,4-Naphthoquinone
Human immunodeficiency virus 1
-
-
0.0374
2,7-dihydroxyisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0353
2-(4-fluorophenyl)-N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)acetamide
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.002 - 0.1967
2-amino-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophene-3-carboxamide
0.00043
2-hydroxy-4H-isoquinoline-1,3-dione
Human Immunodeficiency Virus
-
specific inhibition of isolated RNase H domain and of the full length reverse transcriptase, IC50 value for the isolated RNase H domain is 0.00043 mM
0.1703
2-hydroxy-6-pentadecylbenzoic acid
Human immunodeficiency virus 1
-
-
0.0337
2-hydroxy-6-[(8Z)-pentadec-8-en-1-yl]benzoic acid
Human immunodeficiency virus 1
-
-
0.0072
2-hydroxy-7-(4-hydroxyphenyl)isoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.058
2-hydroxy-7-iodoisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.048
2-hydroxy-7-nitroisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0107
2-hydroxy-7-[4-(trifluoromethyl)phenyl]isoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.00043 - 0.0059
2-hydroxyisoquinoline-1,3(2H,4H)-dione
0.0585
2-[(10Z)-heptadec-10-en-1-yl]-6-hydroxybenzoic acid
Human immunodeficiency virus 1
-
-
0.0005
3,4-dihydroxy-N'-[(E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
Human immunodeficiency virus 1
-
IC50 value is about 0.5 microM
0.0075
4'-chloro-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide
Human immunodeficiency virus 1
P03366
-
0.00002 - 0.001
4-(1-chloro-1,1-difluoromethyl)-4-(2-phenylethynyl)-6-chloro-2H-3,1-benzoxazin-2-one
0.002
4-(dimethylamino)-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
Human immunodeficiency virus 1
P03366
-
0.012
4-methoxy-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
Human immunodeficiency virus 1
P03366
-
0.003
4-tert-butyl-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
Human immunodeficiency virus 1
P03366
-
0.002 - 0.0035
4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid
Human immunodeficiency virus 1
-
a diketo acid RNase H inhibitor, IC50 values for wild-type and mutant enzymes are 0.002-0.0035 mM with all substrates, effect on mutant enzymes, overview
0.0032 - 0.0047
4-[5-(benzoylamino)tien-2-yl]-2,4-dioxobutanoic acid
0.00038
5-chloro-2-hydroxyisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
inhibits the isolated HIV RNase H domain
0.0038 - 0.0296
5-nitrofuran-2-carboxylic acid adamantan-1-carbamoyl methyl ester
0.0026 - 0.0322
5-nitrofuran-2-carboxylic acid [[4-(4-bromophenyl)-thiazol-2-yl]-(tetrahydro-furan-2-yl-methyl)-carbamoyl] methyl ester
0.0086
5-nitrofuran-2-carboxylic acid [[4-(4-bromophenyl)-thiazol-2-yl]-(tetrahydrofuran-2-ylmethyl)-carbamoyl] methyl ester
murine leukemia virus
-
for murine leukemia virus reverse transcriptase
0.0066
7-(3,4-dihydroxyphenyl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0222
7-(4-fluorophenyl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0289
7-chloro-2-hydroxyisoquinoline-1,3(2H,4H)-dione
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0011 - 0.0015
ardimerin digallate
0.000308 - 0.00047
beta-thujaplicinol
0.002
BPH218
Human immunodeficiency virus 1
-
in vitro IC50 value is about 2 microM
0.0000084 - 0.000091
capravirine
0.0005 - 0.0012
dihydroxy benzoyl naphthyl hydrazone
0.0000045 - 0.0000637
efavirenz
0.013
ethyl (5E)-6-[1-(4-fluorobenzyl)-1H-pyrrol-2-yl]-2,4-dioxohex-5-enoate
Human immunodeficiency virus 1
-
-
0.0000076 - 0.0000238
GW8248
0.00146
hyemaloside A
Human immunodeficiency virus 1
-
-
0.00119
hyemaloside C
Human immunodeficiency virus 1
-
-
0.05
illimaquinone
Human immunodeficiency virus 1
-
-
0.015
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-methylbenzohydrazide
Human immunodeficiency virus 1
P03366
-
0.007
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-phenoxybenzohydrazide
Human immunodeficiency virus 1
P03366
-
0.015
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
Human immunodeficiency virus 1
P03366
-
0.005
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide
Human immunodeficiency virus 1
P03366
-
0.0108
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)-3-nitrobenzamide
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0071
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)-4-fluorobenzamide
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0407
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)acetamide
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.0057
N-(2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-7-yl)benzamide
Human immunodeficiency virus 1
-
pH 8.0, 37C
0.003
N-(4-tert-butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone
Human immunodeficiency virus 1
-
IC50 is about 3 microM
0.0032 - 0.005
N-[3-(aminocarbonyl)-4,5-dimethyl-2-thienyl]-2-furancarboxamide
0.000216 - 0.01
nevirapine
0.025
Phosphonoformate
Human immunodeficiency virus 1
-
the inhibitor that bind in the reverse transcriptase polymerase domain inhibits also RNase H activity, IC value for the wild-type enzyme is 0.0015 mM versus substrate DNA-18-nucleotide-RNA hybrid, with the other substrates the IC50 value is above 0.025 mM
0.0000471 - 0.000147
TMC-125
additional information
additional information
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
44 - 50
-
Moloney murine leukemia virus reverse transcriptase shows a curve with the optimal temperature range of around 44-50C
additional information
-
Avian myeloblastosis virus reverse transcriptase shows a curve with the optimal temperature range of around 44-50C
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
44 - 50
-
RNase H activities of Avian myeloblastosis virus reverse transcriptase and the chimeric reverse transcriptases at various temperatures ranging 30-60C
additional information
-
RNase H activities of Moloney murine leukemia virus reverse transcriptase and the chimeric reverse transcriptases at various temperatures ranging 30-60C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Human immunodeficiency virus type 1 group M subtype B
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Simian immunodeficiency virus (isolate Mm142-83)
Simian immunodeficiency virus (isolate Mm142-83)
Simian immunodeficiency virus (isolate Mm142-83)
Simian immunodeficiency virus (isolate Mm142-83)
Simian immunodeficiency virus (isolate Mm142-83)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
15000
-
p15RNaseH(EEF)
15600
1 * 15600, LC11-RNase H1, calculated from amino acid sequence
16000
1 * 16000, LC11-RNase H1, SDS-PAGE
19000
-
gel filtration
20000
-
Ni-Sepharose column chromatography, amino acid calculation
additional information
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 18000, estimateted from amino acid sequence
dimer
HIV-1 reverse transcriptase is a heterodimer consisting of a 66 kDa p66 subunit and a 51 kDa p51 subunit. The two polypeptide chains have 440 N-terminal amino acid residues in common, these comprise four polymerase subdomains: the thumb, palm, fingers, and connection, the C-terminus of p66 contains an additional 120 amino acid residues that form the bulk of the RNH domain
heterodimer
monomer
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in complex with selenium-modified DNA/RNA, sitting drop vapor diffusion method, using 0.1 M MES pH 6.5, 12% (w/v) PEG 20000
crystal structures of full-length HIV-1 reverse transcriptase with a DNA/DNA or RNA/DNA substrate show a distance of about 60 A between the polymerase active site and the RNase H active site
-
enzyme bound to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide, by vapor diffusion in microseeded hanging drops containing equal volumes of protein and reservoir solution containing 50 mM imidazole, pH 6.4, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5% glucose, 11.5% PEG 8000 at 4C, mixing 0.0074 ml of 20 mM inhibitor in DMSO with 0.0025 ml of 20% beta-octyl glucopyranoside, of this solution, 0.0075 ml is combined with 0.065 ml of 40 mg/ml RT and 0.0575 ml of additional RT buffer containing 10 mM Tris, pH 8.0, and 75 mM NaCl on ice, X-ray diffraction structure determination and anaylsis at 3.15 A resolution
more: solution of structure of enzyme is determined by NMR methods in presence of Mg2+
-
purified recombinant mutant Mo-MLV RNase H lacking the putative helix C complexed with the DNA/RNA hybrid substrate, DELTAC monomers and dimers, equilibration against a reservoir solution of 30% PEG 4000 and 0.2 M ammonium sulfate, protein solution, containing 7-10 mg/ml, 10 mM HEPES, pH 7.0, 150 mM NaCl, 5 mM DTT, and 0.1 mM EDTA, is mixed with reservoir solution at pH 5.2-6.0, DELTAC monomer crystallization fails to yield single, large crystals, DELTAC monomer crystals are soaked in 15% PEG 4000, 20% PEG 400, 0.1 M ammonium sulfate, 150 mM NaCl, 1% 2-propanol, 1.25% PEG MME 550, 5 mM MES, pH 6.5, and 0.5 mM zinc sulfate for 5 min, X-ray diffractions tructure determination and analysis at 1.6 A resolution, modelling
-
sitting drop vapor diffusion method, using 0.1 M imidazole pH 8.0, 0.2 M NaCl, 0.4 M NaH2PO4, and 1.6 M K2HPO4
hanging drop vapor diffusion method, using 40% (w/v) PEG1500, 100 mM Na citrate pH 4.7, and 5 mM MgCl2
sitting drop vapor diffusion method, using 27% (w/v) polyethylene glycol 1500 and 0.1 M sodium citrate, pH 4.7
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
58.6
melting temperature in the absence of Mn2+
60
-
for 10 min, does not affect the reaction
63.1
melting temperature in the presence of 1 mM Mn2+
100
-
for 10 min, no activity remains
additional information
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
easily inactivated by oxidation, no activity detected in absence of dithiothreitol or mercaptoethanol
-
134079
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
activity is repidly lost upon repeated thawing
Herpes simplex virus
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
affinity chromatography using Ni-Agarose to enrich for the histidines-tagged proteins and the reverse transcriptase-containing fractions are further purified by carboxyl-methyl Sepharose ion exchange chromatography
GST column chromatography and gel filtration
heparin column chromatography and HiTrap Capto S column chromatography
heterodimeric HIV-1 reverse transcriptase (p66 and p51) are expressed and purified
-
His Trap column chromatography, heparin column chromatography, and Superdex 75 gel filtration
His-Trap HP Ni-NTA column chromatography, and gel filtration
-
HiTrap Q column chromatography and Superdex 200 gel filtration
HiTrap Q column chromatography, Mono Q column chromatography, and Superdex 200pg gel filtration
-
Mono Q column chromatography
Ni-affinity column chromatography and gel filtration
-
Ni2+-Sepharose column chromatography and S200 gel filtration
-
recombinant maltose-binding-protein fusion protein from Escherichia coli strain BL21(DE3), the fused protein is cleaved off, purification by amylose affinity, and several steps of ion exchange chromatography and gel filtration, to over 95% purity, His-tagged isolated RNase H domain from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant viral enzyme from Escherichia coli strain BL21(DE3) by sequential ion exchange chromatography, and gel filtration
-
recombinant wild-type and mutant enzymes, containing a Factor Xa cleavage site and a GST-tag, from Escherichia coli strain BL21(DE3) by glutathione affinity chromatograpy and by cleavage through Factor Xa, followed by anion and cation exchang chromatography, and gel filtration
-
RNase H domain
-
wild-type and chimeric enzymes