3.1.13.2: exoribonuclease H
This is an abbreviated version!
For detailed information about exoribonuclease H, go to the full flat file.
Word Map on EC 3.1.13.2
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3.1.13.2
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strand
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duplex
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nucleic
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rna-dna
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single-stranded
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integrase
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r-loops
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oligodeoxynucleotides
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retrotransposons
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heteroduplexes
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transcriptases
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phosphorothioate
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retroviruses
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polypurine
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moloney
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phosphodiester
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exonuclease
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rna-dependent
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pre-mrnas
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nucleases
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oligodeoxyribonucleotides
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plus-strand
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nnrti
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template-primer
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nucleocapsids
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minus-strand
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dntp
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spliceosome
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myeloblastosis
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thumb
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endonucleolytic
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oligonucleotide-directed
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2'-o-methylated
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nevirapine
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snrnp
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oligoribonucleotide
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primer-template
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okazaki
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nonnucleoside
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rna-directed
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a-form
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efavirenz
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retroelements
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3'-exonuclease
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heteropolymeric
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phosphoramidite
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pregenomic
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hepadnavirus
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hiv-rt
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pharmacology
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medicine
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drug development
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internucleotide
- 3.1.13.2
- strand
- duplex
- nucleic
- rna-dna
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single-stranded
-
integrase
-
r-loops
- oligodeoxynucleotides
-
retrotransposons
- heteroduplexes
- transcriptases
- phosphorothioate
- retroviruses
-
polypurine
-
moloney
-
phosphodiester
-
exonuclease
-
rna-dependent
- pre-mrnas
- nucleases
- oligodeoxyribonucleotides
-
plus-strand
-
nnrti
-
template-primer
-
nucleocapsids
-
minus-strand
- dntp
-
spliceosome
-
myeloblastosis
-
thumb
-
endonucleolytic
-
oligonucleotide-directed
-
2'-o-methylated
- nevirapine
-
snrnp
- oligoribonucleotide
-
primer-template
-
okazaki
-
nonnucleoside
-
rna-directed
-
a-form
- efavirenz
-
retroelements
- 3'-exonuclease
-
heteropolymeric
-
phosphoramidite
-
pregenomic
-
hepadnavirus
- hiv-rt
- pharmacology
- medicine
- drug development
-
internucleotide
Reaction
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid =
Synonyms
3'-to-5' RNase H, HIV RNase H, HIV-1 ribonuclease H, HIV-1 RT ribonuclease H, LC11-RNase H1, More, Prp8, retroviral reverse transcriptase RNaseH, retroviral RNase H, reverse transcriptase ribonuclease H, reverse transcriptase-associated ribonuclease H, ribonuclease H, RNase H, RNase H1, RNase HI, RNaseH, RNH, RNH1, RT RNase H, RT/RNase H, T4 RNase H, Ta11
ECTree
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General Information
General Information on EC 3.1.13.2 - exoribonuclease H
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evolution
malfunction
physiological function
additional information
Tequatrovirus T4
RNase H belongs to the eukaryotic Mre11/Rad50 (MR) and bacterial SbcCD complex family. The crystal structure of T4 RNase H shows a close homology to flap endonucleases of the FEN-1 family rather than RNase H family. FEN-1 is a family of structure-specific 5'-nucleases, which is conserved from bacteriophage to humans
evolution
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RNaseH enzymes belong to the nucleotidyl transferase superfamily whose members share a similar protein fold and catalytic mechanism
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inhibition of hepatitis B virus (HBV) replication by N-hydroxyisoquinolinedione and N-hydroxypyridinedione ribonuclease H inhibitors. Blocking the HBV RNaseH activity prevents removal of the RNA strand from the minus-polarity DNA strand, resulting in an accumulation of RNA:DNA heteroduplexes
malfunction
Tequatrovirus T4
the V43I substitution increases the ratio between exonuclease (EC 3.1.13.2) and endonuclease (EC 3.1.99.) activities of RNase H whereas L242I substitution does not affect the nuclease activity of RNase H in vitro. The Das13 mutant of RNase H has substitutions of valine 43 and leucine 242 with isoleucines. Both mutations are necessary for the full das mutant effect in vivo. The V43I substitution may lead to disposition of H4 helix, responsible for the interaction with the first base pairs of 5' end of branched DNA. These structural changes may affect unwinding of the first base pairs of gapped or nicked DNA generating a short flap and therefore may stabilize the DNA-enzyme complex. The L242I substitution does not affect the structure of RNase H and its role in providing the das-effect remains unclear
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among the activities of herpes simplex virus 1 DNA polymerase (HSV-1 Pol) is an intrinsic RNase H activity that cleaves RNA from RNA-DNA hybrids. The wild-type HSV-1 Pol is able to cleave RNA from the annealed RNA-DNA hairpin template, but only detectably with a 3' RNA terminus in a 3'-to-5' direction and at a rate lower than that of the exonuclease activity. These results suggest that HSV-1 Pol does not have an RNase H separable from its 3'-to-5' exonuclease activity and that this activity prefers DNA degradation over degradation of RNA from RNA-DNA hybrids. No RNase H activity of HSV-1 DNA polymerase on RNA-DNA hybrids with 5' RNA termini
physiological function
Tequatrovirus T4
RNase H is a 5'-nuclease required to remove RNA primers from lagging strand fragments during DNA replication. It forms the gp46/47 enzyme complex consisting of a DNA-activated ATPase, an ssDNA endonuclease and a 3'-5' dsDNA exonuclease
physiological function
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the endonucleolytic RNaseH activity (EC 3.1.26.4) requires an DNA:RNA duplex 14 nt or more and cannot tolerate a stem-loop in either the RNA or DNA strands. It tolerates a nick in the DNA strand but not a gap. The RNaseH has no obvious sequence specificity or positional dependence within the RNA, and it cuts the RNA at multiple positions even within the minimal 14 nt duplex. The RNaseH also possesses a processive 3'-5' exoribonuclease activity (EC 3.1.13.2) that is slower than the endonucleolytic reaction. The HBV reverse transcription mechanism features an initial endoribonucleolytic cut, 3'-5' degradation of RNA, and a sequence-independent terminal RNA cleavage
physiological function
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the endonucleolytic RNaseH activity (EC 3.1.26.4) requires an DNA:RNA duplex 14 nt or more and cannot tolerate a stem-loop in either the RNA or DNA strands. It tolerates a nick in the DNA strand but not a gap. The RNaseH has no obvious sequence specificity or positional dependence within the RNA, and it cuts the RNA at multiple positions even within the minimal 14 nt duplex. The RNaseH also possesses a processive 3'-5' exoribonuclease activity (EC 3.1.13.2) that is slower than the endonucleolytic reaction. The RNaseH is one of two enzymatically active domains on the HBV polymerase that synthesizes the partially double-stranded DNA genome via reverse transcription. The reverse transcriptase (RT) domain of the polymerase protein copies the pregenomic RNA (pgRNA) template to form the minus-polarity DNA strand. The RNaseH recognizes RNA:DNA heteroduplexes that are formed during minus-polarity DNA synthesis and degrades the RNA strand. The polymerase then synthesizes the positive polarity DNA strand, but it typically arrests after making only about 50% of the plus-polarity DNA strand. Both enzymatic activities of the polymerase are required for synthesis of the HBV genome
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HSV-1 Pol contains four domains: the pre-NH2-terminal domain, the NH2-terminal domain, the 3'-to-5' exonuclease (Exo) domain, and the polymerase domain, composed of the palm, finger, and thumb subdomains
additional information
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the RNaseH active site contains four conserved carboxylates (the DEDD motif) that coordinate two divalent cations, usually Mg2+. The RNA cleavage mechanism requires both cations to promote a hydroxyl-mediated nucleophilic scission reaction