EzCatDB: M00166

DB codeM00166
RLCP classification1.13.200.966
3.103.90021.1120
CATH domainDomain 11.10.150.90
Domain 21.10.375.-
Domain 31.10.1200.-
Domain 44.10.60.-
Domain 5-.-.-.-
Domain 62.40.70.10Catalytic domain
Domain 7-.-.-.-
Domain 83.10.10.10
Domain 93.30.70.270Catalytic domain
Domain 103.30.70.270
Domain 113.30.70.270
Domain 123.30.420.10Catalytic domain
Domain 131.10.10.200
Domain 143.30.420.10
Domain 152.30.30.-
Domain 16-.-.-.-
E.C.3.4.23.47,2.7.7.49,2.7.7.7,3.1.26.4

CATH domainRelated DB codes (homologues)
1.10.10.200M00206
2.40.70.10D00471,D00436,D00438,D00439,D00440,D00441,D00442,D00443,D00437,D00444,D00423,D00445,D00484,M00206,D00231,D00529
3.10.10.10M00206,M00135,M00146
3.30.420.10M00206,T00252,M00019,M00020,M00055,M00135,M00146,M00173,M00175,M00186
3.30.70.270M00206,M00019,M00135,M00146,M00209

Enzyme Name
Swiss-protKEGG

P04584
Protein nameGag-Pol polyproteinHIV-2 retropepsin
   (EC 3.4.23.47)
RNA-directed DNA polymerase
   (EC 2.7.7.49)
DNA nucleotidyltransferase (RNA-directed)
   (EC 2.7.7.49)
reverse transcriptase
   (EC 2.7.7.49)
revertase
   (EC 2.7.7.49)
RNA-dependent deoxyribonucleate nucleotidyltransferase
   (EC 2.7.7.49)
RNA revertase
   (EC 2.7.7.49)
RNA-dependent DNA polymerase
   (EC 2.7.7.49)
RNA-instructed DNA polymerase
   (EC 2.7.7.49)
RT
   (EC 2.7.7.49)
DNA-directed DNA polymerase
   (EC 2.7.7.7)
DNA polymerase I
   (EC 2.7.7.7)
DNA polymerase II
   (EC 2.7.7.7)
DNA polymerase III
   (EC 2.7.7.7)
DNA polymerase alpha
   (EC 2.7.7.7)
DNA polymerase beta
   (EC 2.7.7.7)
DNA polymerase gamma
   (EC 2.7.7.7)
DNA nucleotidyltransferase (DNA-directed)
   (EC 2.7.7.7)
DNA nucleotidyltransferase (DNA-directed)
   (EC 2.7.7.7)
deoxyribonucleate nucleotidyltransferase
   (EC 2.7.7.7)
deoxynucleate polymerase
   (EC 2.7.7.7)
deoxyribonucleic acid duplicase
   (EC 2.7.7.7)
deoxyribonucleic acid polymerase
   (EC 2.7.7.7)
deoxyribonucleic duplicase
   (EC 2.7.7.7)
deoxyribonucleic polymerase
   (EC 2.7.7.7)
deoxyribonucleic polymerase I
   (EC 2.7.7.7)
DNA duplicase
   (EC 2.7.7.7)
DNA nucleotidyltransferase
   (EC 2.7.7.7)
DNA polymerase
   (EC 2.7.7.7)
DNA replicase
   (EC 2.7.7.7)
DNA-dependent DNA polymerase
   (EC 2.7.7.7)
duplicase
   (EC 2.7.7.7)
Klenow fragment
   (EC 2.7.7.7)
sequenase
   (EC 2.7.7.7)
Taq DNA polymerase
   (EC 2.7.7.7)
Taq Pol I
   (EC 2.7.7.7)
Tca DNA polymerase
   (EC 2.7.7.7)
calf thymus ribonuclease H
   (EC 3.1.26.4)
endoribonuclease H (calf thymus)
   (EC 3.1.26.4)
RNase H
   (EC 3.1.26.4)
RNA*DNA hybrid ribonucleotidohydrolase
   (EC 3.1.26.4)
hybrid ribonuclease
   (EC 3.1.26.4)
hybridase
   (EC 3.1.26.4)
hybridase (ribonuclease H)
   (EC 3.1.26.4)
ribonuclease H
   (EC 3.1.26.4)
hybrid nuclease
   (EC 3.1.26.4)
SynonymsPr160Gag-Pol
ContainsMatrix protein p17
(MA)
Capsid protein p24
(CA)
Spacer peptide p2
Nucleocapsid protein p7
(NC)
Transframe peptide
(TF)
p6-pol
(p6*)
Protease
   EC 3.4.23.47
Retropepsin PR
Reverse transcriptase/ribonuclease H
   EC 2.7.7.49
   EC 2.7.7.7
   EC 3.1.26.4
p66 RT
p51 RT
p15
Integrase
(IN)

KEGG pathways
MAP codePathwaysE.C.
MAP00230Purine metabolism2.7.7.7
MAP00240Pyrimidine metabolism2.7.7.7

Swiss-prot:Accession NumberP04584
Entry namePOL_HV2RO
ActivityEndonucleolytic cleavage to 5''- phosphomonoester.,Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).,Endopeptidase for which the P1 residue is preferably hydrophobic.
SubunitMatrix protein p17 is a trimer. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. The integrase is a homodimer and possibly a homotetramer (By similarity).
Subcellular locationMatrix protein p17: Virion (Potential). Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane, Lipid-anchor (Potential). Note=Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity).,Capsid protein p24: Virion (Potential).,Nucleocapsid protein p7: Virion (Potential).,Reverse transcriptase/ribonuclease H: Virion (Potential).,Integrase: Virion (Potential). Nucleus (Potential). Cytoplasm (Potential). Note=Nuclear at initial phase, cytoplasmic at assembly (Potential).
CofactorBinds 2 magnesium ions for reverse transcriptase polymerase activity (By similarity).,Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding (By similarity).,Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions (By similarity).


CofactorsSubstratesProductsintermediates
KEGG-idC00305C00038C00017C00012C00677C00039C00046C00001C00017C00012C00013C00039C00960I00136
E.C.2.7.7.49,2.7.7.7,3.1.26.4
3.4.23.473.4.23.472.7.7.49,2.7.7.72.7.7.49,2.7.7.73.1.26.43.1.26.4,3.4.23.473.4.23.473.4.23.472.7.7.49,2.7.7.72.7.7.49,2.7.7.73.1.26.43.4.23.47
CompoundMagnesiumZincProteinPeptideDeoxynucleoside triphosphateDNA(n)RNAH2OProteinPeptidePyrophosphateDNA(n+1)RNA 5'-phosphateAmino-diol-tetrahedral intermediate
Typedivalent metal (Ca2+, Mg2+)heavy metalpeptide/proteinpeptide/proteinnucleotidenucleic acidsnucleic acidsH2Opeptide/proteinpeptide/proteinphosphate group/phosphate ionnucleic acidsnucleic acids,phosphate group/phosphate ion
1hiiAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:C20
1hshAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:MK1
1hshCUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:MK1
1hsiAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1idaAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:0PO
1idbAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:0DO
1ivpAUnboundUnboundUnboundAnalogue:1ZKUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1ivqAUnboundUnboundUnboundAnalogue:0PXUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1jldAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:0PP
2hpeAUnboundUnboundUnboundBound:UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNKUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2hpfAUnboundUnboundUnboundBound:UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNKUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2mipAUnboundUnboundUnboundAnalogue:PHE-VAL-PHE-LEU-GLU-ILE-NH2(chain E,G)UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2mipCUnboundUnboundUnboundAnalogue:PHE-VAL-PHE-LEU-GLU-ILE-NH2(chain F,H)UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3upjAUnboundUnboundUnboundAnalogue:U03UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
4upjAUnboundUnboundUnboundAnalogue:U04UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
5upjAUnboundUnboundUnboundAnalogue:UINUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
6upjAUnboundUnboundUnboundAnalogue:NIUUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1hiiBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1hshBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1hshDUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1hsiBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1idaBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1idbBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1ivpBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1ivqBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1jldBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2hpeBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2hpfBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2mipBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2mipDUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3upjBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
4upjBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
5upjBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
6upjBUnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2A01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2B01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2A02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2B02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2A03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2B03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2A04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2B04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1mu2A05UnboundUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kA01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kB01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kE01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kF01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kI01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kJ01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kM01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kN01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kQ01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kR01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kU01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kV01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kY01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kZ01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kc01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kd01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kg01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kh01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kk01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kl01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9ko01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kp01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9ks01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kt01UnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1aubAUnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1e0eAUnboundBound:_ZNUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kA02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kB02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kE02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kF02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kI02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kJ02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kM02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kN02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kQ02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kR02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kU02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kV02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kY02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kZ02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kc02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kd02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kg02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kh02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kk02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kl02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9ko02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kp02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9ks02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
3f9kt02Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1aub & literature [6], M00135, M00146
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
1hiiAASP 25


(EC 3.4.23.47)
1hshAASP 25


(EC 3.4.23.47)
1hshCASP 25


(EC 3.4.23.47)
1hsiAASP 25


(EC 3.4.23.47)
1idaAASP 25


(EC 3.4.23.47)
1idbAASP 25


(EC 3.4.23.47)
1ivpAASP 25


(EC 3.4.23.47) mutant K57L
1ivqAASP 25


(EC 3.4.23.47) mutant K57L
1jldAASP 25


(EC 3.4.23.47)
2hpeAASP 25


(EC 3.4.23.47) mutant K57L
2hpfAASP 25


(EC 3.4.23.47) mutant K57L
2mipAASP 25


(EC 3.4.23.47)
2mipCASP 25


(EC 3.4.23.47)
3upjAASP 25


(EC 3.4.23.47) mutant K57L
4upjAASP 25


(EC 3.4.23.47) mutant K57L
5upjAASP 25


(EC 3.4.23.47) mutant K57L
6upjAASP 25


(EC 3.4.23.47) mutant K57L
1hiiBASP 25


(EC 3.4.23.47)
1hshBASP 25


(EC 3.4.23.47)
1hshDASP 25


(EC 3.4.23.47)
1hsiBASP 25


(EC 3.4.23.47)
1idaBASP 25


(EC 3.4.23.47)
1idbBASP 25


(EC 3.4.23.47)
1ivpBASP 25


(EC 3.4.23.47) mutant K57L
1ivqBASP 25


(EC 3.4.23.47) mutant K57L
1jldBASP 25


(EC 3.4.23.47)
2hpeBASP 25


(EC 3.4.23.47) mutant K57L
2hpfBASP 25


(EC 3.4.23.47) mutant K57L
2mipBASP 25


(EC 3.4.23.47)
2mipDASP 25


(EC 3.4.23.47)
3upjBASP 25


(EC 3.4.23.47) mutant K57L
4upjBASP 25


(EC 3.4.23.47) mutant K57L
5upjBASP 25


(EC 3.4.23.47) mutant K57L
6upjBASP 25


(EC 3.4.23.47) mutant K57L
1mu2A01



1mu2B01



1mu2A02
ASP 110;ASP 185;ASP 186(Magnesium binding)
ASP 113;ALA 114
(EC 2.7.7.49 & 2.7.7.7)
1mu2B02



1mu2A03



1mu2B03



1mu2A04



1mu2B04



1mu2A05
ASP 442;ASP 497(Magnesium binding)

(EC 3.1.26.4)
3f9kA01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kB01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kE01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kF01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kI01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kJ01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kM01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kN01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kQ01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kR01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kU01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kV01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kY01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kZ01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kc01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kd01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kg01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kh01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kk01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kl01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9ko01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kp01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9ks01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kt01
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
1aubA
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
1e0eA
HIS 12;HIS 16;CYS 40;CYS 43(Zinc binding)

(integrase)
3f9kA02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kB02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kE02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kF02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kI02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kJ02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kM02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kN02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kQ02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kR02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kU02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kV02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kY02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kZ02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kc02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kd02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kg02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kh02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kk02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kl02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9ko02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kp02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9ks02
ASP 64;ASP 116(Magnesium binding)

(integrase)
3f9kt02
ASP 64;ASP 116(Magnesium binding)

(integrase)


references
[1]
PubMed ID1812757
JournalAdv Exp Med Biol
Year1991
Volume306
Pages549-53
AuthorsGustchina A, Weber IT, Wlodawer A
TitleMolecular modeling of the HIV-2 protease.
[2]
PubMed ID2001747
JournalFEBS Lett
Year1991
Volume279
Pages356-60
AuthorsTozser J, Gustchina A, Weber IT, Blaha I, Wondrak EM, Oroszlan S
TitleStudies on the role of the S4 substrate binding site of HIV proteinases.
[3]
CommentsTheoretical model
PubMed ID1946342
JournalProteins
Year1991
Volume10
Pages325-39
AuthorsGustchina A, Weber IT
TitleComparative analysis of the sequences and structures of HIV-1 and HIV-2 proteases.
Related PDB1phv,2phv
[4]
PubMed ID8241159
JournalBiochemistry
Year1993
Volume32
Pages13054-60
AuthorsZhao B, Winborne E, Minnich MD, Culp JS, Debouck C, Abdel-Meguid SS
TitleThree-dimensional structure of a simian immunodeficiency virus protease/inhibitor complex. Implications for the design of human immunodeficiency virus type 1 and 2 protease inhibitors.
[5]
PubMed ID8087563
JournalBioorg Med Chem
Year1993
Volume1
Pages415-22
AuthorsSui Z, Salto R, Li J, Craik C, Ortiz de Montellano PR
TitleInhibition of the HIV-1 and HIV-2 proteases by curcumin and curcumin boron complexes.
[6]
PubMed ID8514751
JournalJ Biol Chem
Year1993
Volume268
Pages13103-9
AuthorsMulichak AM, Hui JO, Tomasselli AG, Heinrikson RL, Curry KA, Tomich CS, Thaisrivongs S, Sawyer TK, Watenpaugh KD
TitleThe crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 86-184.
Medline ID93391360
PubMed ID8378311
JournalProc Natl Acad Sci U S A
Year1993
Volume90
Pages8387-91
AuthorsTong L, Pav S, Pargellis C, Do F, Lamarre D, Anderson PC
TitleCrystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with a reduced amide inhibitor and comparison with HIV-1 protease structures.
Related PDB2mip
Related Swiss-protP04584
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 86-184 IN COMPLEX WITH INHIB.
Medline ID95014470
PubMed ID7929352
JournalJ Biol Chem
Year1994
Volume269
Pages26344-8
AuthorsChen Z, Li Y, Chen E, Hall DL, Darke PL, Culberson C, Shafer JA, Kuo LC
TitleCrystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases.
Related PDB1hsh,1hsi
Related Swiss-protP04584
[9]
PubMed ID8035428
JournalJ Med Chem
Year1994
Volume37
Pages2206-15
AuthorsOprea TI, Waller CL, Marshall GR
TitleThree-dimensional quantitative structure-activity relationship of human immunodeficiency virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes.
[10]
PubMed ID7526778
JournalAnnu Rev Biochem
Year1994
Volume63
Pages133-73
AuthorsKatz RA, Skalka AM
TitleThe retroviral enzymes.
[11]
CommentsX-ray crystallography
PubMed ID7783120
JournalJ Med Chem
Year1995
Volume38
Pages1884-91
AuthorsRomines KR, Watenpaugh KD, Tomich PK, Howe WJ, Morris JK, Lovasz KD, Mulichak AM, Finzel BC, Lynn JC, Horng MM, et al
TitleUse of medium-sized cycloalkyl rings to enhance secondary binding: discovery of a new class of human immunodeficiency virus (HIV) protease inhibitors.
Related PDB5upj,6upj
[12]
CommentsX-ray crystallography
PubMed ID7658450
JournalJ Med Chem
Year1995
Volume38
Pages3624-37
AuthorsThaisrivongs S, Watenpaugh KD, Howe WJ, Tomich PK, Dolak LA, Chong KT, Tomich CC, Tomasselli AG, Turner SR, Strohbach JW, et al
TitleStructure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors.
Related PDB3upj,4upj
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 86-184 IN COMPLEX WITH INHIB.
Medline ID95338600
PubMed ID7613867
JournalStructure
Year1995
Volume3
Pages381-9
AuthorsPriestle JP, Fassler A, Rosel J, Tintelnot-Blomley M, Strop P, Grutter MG
TitleComparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor.
Related PDB1hii
Related Swiss-protP04584
[14]
PubMed ID7743130
JournalStructure
Year1995
Volume3
Pages33-40
AuthorsTong L, Pav S, Mui S, Lamarre D, Yoakim C, Beaulieu P, Anderson PC
TitleCrystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere.
[15]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 86-184 IN COMPLEX WITH INHIB.
Medline ID97359919
PubMed ID9216835
JournalJ Med Chem
Year1997
Volume40
Pages2164-76
AuthorsBeaulieu PL, Wernic D, Abraham A, Anderson PC, Bogri T, Bousquet Y, Croteau G, Guse I, Lamarre D, Liard F, Paris W, Thibeault D, Pav S, Tong L
TitlePotent HIV protease inhibitors containing a novel (hydroxyethyl)amide isostere.
Related PDB1jld
Related Swiss-protP04584
[16]
PubMed ID9209317
JournalLeukemia
Year1997
Volume11 Suppl 3
Pages120-2
AuthorsPichova I, Weber J, Litera J, Konvalinka J, Vondrasek J, Soucek M, Strop P, Majer P, Heuser AM, Kraeusslich HG
TitlePeptide inhibitors of HIV-1 and HIV-2 proteases: a comparative study.
[17]
PubMed ID9368756
JournalCurr Biol
Year1997
Volume7
Pages739-46
AuthorsEijkelenboom AP, van den Ent FM, Vos A, Doreleijers JF, Hard K, Tullius TD, Plasterk RH, Kaptein R, Boelens R
TitleThe solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc.
[18]
PubMed ID9692985
JournalBiochemistry
Year1998
Volume37
Pages10928-36
AuthorsSwairjo MA, Towler EM, Debouck C, Abdel-Meguid SS
TitleStructural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease.
[19]
PubMed ID9557677
JournalJ Virol
Year1998
Volume72
Pages3916-24
Authorsvan den Ent FM, Vos A, Plasterk RH
TitleMutational scan of the human immunodeficiency virus type 2 integrase protein.
[20]
PubMed ID10491141
JournalEur J Biochem
Year1999
Volume264
Pages921-9
AuthorsBoross P, Bagossi P, Copeland TD, Oroszlan S, Louis JM, Tozser J
TitleEffect of substrate residues on the P2' preference of retroviral proteinases.
[21]
PubMed ID10631984
JournalProtein Sci
Year1999
Volume8
Pages2686-96
AuthorsLescar J, Brynda J, Rezacova P, Stouracova R, Riottot MM, Chitarra V, Fabry M, Horejsi M, Sedlacek J, Bentley GA
TitleInhibition of the HIV-1 and HIV-2 proteases by a monoclonal antibody.
[22]
CommentsNMR structure
PubMed ID11101216
JournalJ Biomol NMR
Year2000
Volume18
Pages119-28
AuthorsEijkelenboom AP, van den Ent FM, Wechselberger R, Plasterk RH, Kaptein R, Boelens R
TitleRefined solution structure of the dimeric N-terminal HHCC domain of HIV-2 integrase.
Related PDB1aub
[23]
PubMed ID11591344
JournalStructure (Camb)
Year2001
Volume9
Pages887-95
AuthorsRezacova P, Lescar J, Brynda J, Fabry M, Horejsi M, Sedlacek J, Bentley GA
TitleStructural basis of HIV-1 and HIV-2 protease inhibition by a monoclonal antibody.
[24]
PubMed ID12386343
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages14410-5
AuthorsRen J, Bird LE, Chamberlain PP, Stewart-Jones GB, Stuart DI, Stammers DK
TitleStructure of HIV-2 reverse transcriptase at 2.35-A resolution and the mechanism of resistance to non-nucleoside inhibitors.
[25]
PubMed ID12511797
JournalJ Synchrotron Radiat
Year2003
Volume10
Pages86-95
AuthorsFeiters MC, Eijkelenboom AP, Nolting HF, Krebs B, van den Ent FM, Plasterk RH, Kaptein R, Boelens R
TitleX-ray absorption spectroscopic studies of zinc in the N-terminal domain of HIV-2 integrase and model compounds.
[26]
PubMed ID19132083
JournalPLoS Pathog
Year2009
Volume5
Pagese1000259
AuthorsHare S, Shun MC, Gupta SS, Valkov E, Engelman A, Cherepanov P
TitleA novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75.
Related PDB3f9k

comments
The protein, POL polyprotein (Swiss-prot; P04584) from HIV-2, is composed of the following enzymes, protease (E.C. 3.4.23.47), reverse transcriptase (E.C. 2.7.7.49 & 2.7.7.7), ribonuclease H (E.C. 3.1.26.4) and integrase.
This entry corresponds to the protease domain (residues 86-184), and the reverse transcriptase and ribonuclease H (residues 613-1171) and a non-catalytic region of integrase (residues 1224-1464) of this protein (Swiss-prot;P04584).
###
The protease domain form a homodimer to function as an enzyme. This enzyme domain belongs to the peptidase family-A2.
The homodimer of this domain contains a catalytic dyad, composed of two aspartic acid residues, suggesting that it has a similar catalytic mechanism to that of pepsin (D00436 in EzCatDB).
###
According to the literature [17], the C-terminal structure (PDB;1e0e) corresponds to the N-terminal domain of integrase, which catalyzes cleavage of viral DNA, and integration of the cleaved DNA into the target DNA. However, the catalytic domain of this enzyme has not been determined yet.
The paper [10] mentioned that zinc binding in this domain stabilizes its structure, instead of contributing to the catalysis.
###
On the other hand, the N-terminal domains of 1mu2 (PDB) correspond to reverse transcriptase (E.C. 2.7.7.49), whilst the fifth domain of 1mu2 corresponds to ribonuclease H (E.C. 3.1.26.4). Considering the structural similarity to that of M00146, the ribonuclease H must have got a binding site for magnesium or manganese ion at the catalytic site.
Since the catalytic site of the reverse transcriptase (E.C. 2.7.7.49) is homologous to that of its homologous enzyme from Moloney murine leukemia virus (M00135 in EzCatDB), its catalytic mechanism must be similar to that of the homologous enzyme.

createdupdated
2002-09-102012-06-29
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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