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Crystal structure of the Prototype Foamy Virus (PFV) S217H mutant intasome in complex with magnesium and Dolutegravir (S/GSK1349572)

Source organism: Human spumaretrovirus
Biochemical function: nucleic acid binding
Biological process: DNA integration
Cellular component: not assigned

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EC 3.1.26.4: Ribonuclease H

Reaction catalysed:
Endonucleolytic cleavage to 5'-phosphomonoester.
Systematic name:
-
Alternative Name(s):
  • Calf thymus ribonuclease H
  • Endoribonuclease H
  • Endoribonuclease H (calf thymus)
  • Hybrid nuclease
  • Hybrid ribonuclease
  • Hybridase
  • Hybridase (ribonuclease H)
  • RNA*DNA hybrid ribonucleotidohydrolase
  • RNase H

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)
PF18103
Domain description: Retroviral integrase C-terminal SH3 domain
Occurring in:
  1. Integrase
The deposited structure of PDB entry 3s3n contains 2 copies of Pfam domain PF18103 (Retroviral integrase C-terminal SH3 domain) in Integrase. Showing 1 copy in chain A.

PF00665
Domain description: Integrase core domain
Occurring in:
  1. Integrase
The deposited structure of PDB entry 3s3n contains 2 copies of Pfam domain PF00665 (Integrase core domain) in Integrase. Showing 1 copy in chain A.

PF17921
Domain description: Integrase zinc binding domain
Occurring in:
  1. Integrase
The deposited structure of PDB entry 3s3n contains 2 copies of Pfam domain PF17921 (Integrase zinc binding domain) in Integrase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001584
Domain description: Integrase, catalytic core
Occurring in:
  1. Integrase
IPR040903
Domain description: Retroviral integrase, C-terminal SH3 domain
Occurring in:
  1. Integrase
IPR036397
Domain description: Ribonuclease H superfamily
Occurring in:
  1. Integrase
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. Integrase
IPR041588
Domain description: Integrase zinc-binding domain
Occurring in:
  1. Integrase

Structure domains

CATH CATH domains
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. Integrase
The deposited structure of PDB entry 3s3n contains 2 copies of CATH domain 3.30.420.10 (Nucleotidyltransferase; domain 5) in Integrase. Showing 1 copy in chain A.
2.30.30.140
Class: Mainly Beta
Architecture: Roll
Topology: SH3 type barrels.
Homology: SH3 type barrels.
Occurring in:
  1. Integrase
The deposited structure of PDB entry 3s3n contains 1 copy of CATH domain 2.30.30.140 (SH3 type barrels.) in Integrase. Showing 1 copy in chain A.
6.10.20.110
Class: Special
Architecture: Helix non-globular
Topology: Arc Repressor Mutant, subunit A
Homology: Arc Repressor Mutant, subunit A
Occurring in:
  1. Integrase
The deposited structure of PDB entry 3s3n contains 1 copy of CATH domain 6.10.20.110 (Arc Repressor Mutant, subunit A) in Integrase. Showing 1 copy in chain A.
1.10.340.70
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Endonuclease III; domain 1
Homology: Endonuclease III; domain 1
Occurring in:
  1. Integrase
The deposited structure of PDB entry 3s3n contains 1 copy of CATH domain 1.10.340.70 (Endonuclease III; domain 1) in Integrase. Showing 1 copy in chain A.

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