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Gag-Pol polyprotein



Human immunodeficiency virus type 1 group M subtype D (isolate Z6) (HIV-1)
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli


Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.By similarity


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi12Magnesium; catalytic; for integrase activityBy similarity1


Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi83 – 130Integrase-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

GO - Biological processi


Molecular functionDNA-binding, Endonuclease, Hydrolase, Nuclease
Biological processDNA integration, DNA recombination, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Viral genome integration, Virus entry into host cell
LigandLipid-binding, Metal-binding

Protein family/group databases


Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Alternative name(s):
Cleaved into the following chain:
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
Gene namesi
OrganismiHuman immunodeficiency virus type 1 group M subtype D (isolate Z6) (HIV-1)
Taxonomic identifieri11708 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]

Pathology & Biotechi

Keywords - Diseasei


PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_0000261289‹1 – 148Gag-Pol polyproteinAdd BLAST›148
ChainiPRO_0000042448‹1 – 148IntegraseBy similarityAdd BLAST›148

Post-translational modificationi

Specific enzymatic cleavages by the viral protease yield mature proteins.By similarity


Subunit structurei

Matrix protein p17: Homotrimer; further assembles as hexamers of trimers (By similarity). Matrix protein p17: Interacts with gp41 (via C-terminus) (By similarity). Matrix protein p17: interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group (By similarity). Matrix protein p17: interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly (By similarity). Matrix protein p17: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase (By similarity). Capsid protein p24: Homodimer; the homodimer further multimerizes as homohexamers or homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA (By similarity); This interaction stabilizes the capsid. Capsid protein p24: Interacts with human NUP153 (By similarity). Capsid protein p24: Interacts with host PDZD8; this interaction stabilizes the capsid (By similarity). Capsid protein p24: Interacts with monkey TRIM5; this interaction destabilizes the capsid (By similarity).Protease: Homodimer, whose active site consists of two apposed aspartic acid residues. Reverse transcriptase/ribonuclease H: 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. Integrase: Homodimer; possibly can form homotetramer. Integrase: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Integrase: Interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1. Integrase: Interacts with human KPNA3; this interaction might play a role in nuclear import of the pre-integration complex (By similarity). Integrase: Interacts with human NUP153; this interaction might play a role in nuclear import of the pre-integration complex (By similarity).By similarity


Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi82 – 88Combined sources7
Beta strandi93 – 115Combined sources23
Beta strandi117 – 121Combined sources5
Helixi122 – 124Combined sources3
Beta strandi125 – 129Combined sources5

3D structure databases

Select the link destinations:
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum

Miscellaneous databases


Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini‹1 – 64Integrase catalyticPROSITE-ProRule annotationAdd BLAST›64

Family and domain databases

Gene3Di2.30.30.10. 1 hit.
3.30.420.10. 1 hit.
InterProiView protein in InterPro
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR012337. RNaseH-like_dom.
PfamiView protein in Pfam
PF00552. IN_DBD_C. 1 hit.
SUPFAMiSSF50122. SSF50122. 1 hit.
SSF53098. SSF53098. 1 hit.
PROSITEiView protein in PROSITE
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.


Sequence statusi: Fragment.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04586-1 [UniParc]FASTAAdd to basket

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60 70 80 90 100
110 120 130 140
Mass (Da):16,840
Last modified:August 13, 1987 - v1

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Non-terminal residuei11

Sequence databases

Select the link destinations:
Links Updated
K03458 Genomic RNA. Translation: AAA45376.1.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiPOL_HV1Z6
AccessioniPrimary (citable) accession number: P04586
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: May 10, 2017
This is version 131 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program


Keywords - Technical termi



  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references