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Crystal structure of V108I mutant HIV-1 reverse transcriptase in complex with nevirapine

Source organism: Human immunodeficiency virus 1
Biochemical function: RNA-directed DNA polymerase activity
Biological process: RNA-templated DNA biosynthetic process
Cellular component: not assigned

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EC 3.4.23.16: HIV-1 retropepsin

Reaction catalysed:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Alternative Name(s):
  • Gag protease
  • HIV aspartyl protease
  • HIV proteinase
  • HIV-1 protease
  • HIV-2 protease
  • Human immunodeficiency virus type 1 protease
  • Retroproteinase

EC 3.1.26.13: Retroviral ribonuclease H

Reaction catalysed:
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Systematic name:
-
Alternative Name(s):
  • HIV RNase H
  • RT/RNase H
  • Retroviral reverse transcriptase RNaseH

EC 3.1.13.2: Exoribonuclease H

Reaction catalysed:
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Systematic name:
-

EC 2.7.7.7: DNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • DNA duplicase
  • DNA nucleotidyltransferase
  • DNA nucleotidyltransferase (DNA-directed)
  • DNA polymerase
  • DNA polymerase I
  • DNA polymerase II
  • DNA polymerase III
  • DNA polymerase alpha
  • DNA polymerase beta
  • DNA polymerase gamma
  • DNA replicase
  • DNA-dependent DNA polymerase
  • Deoxynucleate polymerase
  • Deoxyribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid duplicase
  • Deoxyribonucleic acid polymerase
  • Deoxyribonucleic duplicase
  • Deoxyribonucleic polymerase
  • Deoxyribonucleic polymerase I
  • Duplicase
  • Klenow fragment
  • Sequenase
  • Taq DNA polymerase
  • Taq Pol I
  • Tca DNA polymerase

EC 2.7.7.49: RNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • DNA nucleotidyltransferase (RNA-directed)
  • RNA revertase
  • RNA-dependent DNA polymerase
  • RNA-dependent deoxyribonucleate nucleotidyltransferase
  • RNA-instructed DNA polymerase
  • RT
  • Reverse transcriptase
  • Revertase

GO terms

Biochemical function:
Biological process:
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF06815
Domain description: Reverse transcriptase connection domain
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF06815 (Reverse transcriptase connection domain) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF06815 (Reverse transcriptase connection domain) in p51 RT. Showing 1 copy in chain B.

PF06817
Domain description: Reverse transcriptase thumb domain
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF06817 (Reverse transcriptase thumb domain) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF06817 (Reverse transcriptase thumb domain) in p51 RT. Showing 1 copy in chain B.

PF00078
Domain description: Reverse transcriptase (RNA-dependent DNA polymerase)
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF00078 (Reverse transcriptase (RNA-dependent DNA polymerase)) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF00078 (Reverse transcriptase (RNA-dependent DNA polymerase)) in p51 RT. Showing 1 copy in chain B.

PF00075
Domain description: RNase H
Occurring in:
  1. Reverse transcriptase/ribonuclease H
The deposited structure of PDB entry 1s1x contains 1 copy of Pfam domain PF00075 (RNase H) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR043128
Domain description: Reverse transcriptase/Diguanylate cyclase domain
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
IPR000477
Domain description: Reverse transcriptase domain
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
IPR002156
Domain description: Ribonuclease H domain
Occurring in:
  1. Reverse transcriptase/ribonuclease H
IPR010659
Domain description: Reverse transcriptase connection
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
IPR010661
Domain description: Reverse transcriptase thumb
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
IPR043502
Domain description: DNA/RNA polymerase superfamily
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
IPR036397
Domain description: Ribonuclease H superfamily
Occurring in:
  1. Reverse transcriptase/ribonuclease H
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. Reverse transcriptase/ribonuclease H

Structure domains

CATH CATH domains
3.30.70.270
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
The deposited structure of PDB entry 1s1x contains 3 copies of CATH domain 3.30.70.270 (Alpha-Beta Plaits) in Reverse transcriptase/ribonuclease H. Showing 3 copies in chain A.
The deposited structure of PDB entry 1s1x contains 3 copies of CATH domain 3.30.70.270 (Alpha-Beta Plaits) in p51 RT. Showing 3 copies in chain B.
3.10.10.10
Class: Alpha Beta
Architecture: Roll
Topology: HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homology: HIV Type 1 Reverse Transcriptase, subunit A, domain 1
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
The deposited structure of PDB entry 1s1x contains 1 copy of CATH domain 3.10.10.10 (HIV Type 1 Reverse Transcriptase; Chain A, domain 1) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.
The deposited structure of PDB entry 1s1x contains 1 copy of CATH domain 3.10.10.10 (HIV Type 1 Reverse Transcriptase; Chain A, domain 1) in p51 RT. Showing 1 copy in chain B.
3.30.420.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Nucleotidyltransferase; domain 5
Homology: Ribonuclease H-like superfamily/Ribonuclease H
Occurring in:
  1. Reverse transcriptase/ribonuclease H
The deposited structure of PDB entry 1s1x contains 1 copy of CATH domain 3.30.420.10 (Nucleotidyltransferase; domain 5) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.
SCOP SCOP annotations
56686
Class: Multi-domain proteins (alpha and beta)
Fold: DNA/RNA polymerases
Superfamily: DNA/RNA polymerases
Occurring in:
  1. Reverse transcriptase/ribonuclease H
  2. p51 RT
The deposited structure of PDB entry 1s1x contains 1 copy of SCOP domain 56686 (Reverse transcriptase) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.
The deposited structure of PDB entry 1s1x contains 1 copy of SCOP domain 56686 (Reverse transcriptase) in p51 RT. Showing 1 copy in chain B.
53099
Class: Alpha and beta proteins (a/b)
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Occurring in:
  1. Reverse transcriptase/ribonuclease H
The deposited structure of PDB entry 1s1x contains 1 copy of SCOP domain 53099 (Ribonuclease H) in Reverse transcriptase/ribonuclease H. Showing 1 copy in chain A.

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