ID   POL_HV2SB               Reviewed;        1462 AA.
AC   P12451; Q85570;
DT   01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   27-MAR-2024, entry version 192.
DE   RecName: Full=Gag-Pol polyprotein;
DE   AltName: Full=Pr160Gag-Pol;
DE   Contains:
DE     RecName: Full=Matrix protein p17;
DE              Short=MA;
DE   Contains:
DE     RecName: Full=Capsid protein p24;
DE              Short=CA;
DE   Contains:
DE     RecName: Full=Spacer peptide 1 {ECO:0000250|UniProtKB:P12497};
DE              Short=SP1;
DE     AltName: Full=p2;
DE   Contains:
DE     RecName: Full=Nucleocapsid protein p7;
DE              Short=NC;
DE   Contains:
DE     RecName: Full=Transframe peptide;
DE              Short=TF;
DE   Contains:
DE     RecName: Full=p6-pol;
DE              Short=p6*;
DE   Contains:
DE     RecName: Full=Protease;
DE              EC=3.4.23.47;
DE     AltName: Full=PR;
DE     AltName: Full=Retropepsin;
DE   Contains:
DE     RecName: Full=Reverse transcriptase/ribonuclease H;
DE              EC=2.7.7.49;
DE              EC=2.7.7.7;
DE              EC=3.1.26.13;
DE     AltName: Full=Exoribonuclease H;
DE              EC=3.1.13.2;
DE     AltName: Full=p66 RT;
DE   Contains:
DE     RecName: Full=p51 RT;
DE   Contains:
DE     RecName: Full=p15;
DE   Contains:
DE     RecName: Full=Integrase;
DE              Short=IN;
DE              EC=2.7.7.- {ECO:0000250|UniProtKB:P04585};
DE              EC=3.1.-.- {ECO:0000250|UniProtKB:P04585};
GN   Name=gag-pol;
OS   Human immunodeficiency virus type 2 subtype A (isolate SBLISY) (HIV-2).
OC   Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC   Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus;
OC   Human immunodeficiency virus 2.
OX   NCBI_TaxID=11718;
OH   NCBI_TaxID=9606; Homo sapiens (Human).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=2648404; DOI=10.1073/pnas.86.7.2433;
RA   Franchini G., Fargnoli K.A., Giombini F., Jagodzinski L.L., de Rossi A.,
RA   Bosch M., Biberfeld G., Fenyo A.M., Albert J., Gallo R.C., Wong-Staal F.;
RT   "Molecular and biological characterization of a replication competent human
RT   immunodeficiency type 2 (HIV-2) proviral clone.";
RL   Proc. Natl. Acad. Sci. U.S.A. 86:2433-2437(1989).
RN   [2]
RP   REVIEW.
RX   PubMed=8791726; DOI=10.1007/978-3-642-80145-7_4;
RA   Vogt V.M.;
RT   "Proteolytic processing and particle maturation.";
RL   Curr. Top. Microbiol. Immunol. 214:95-131(1996).
RN   [3]
RP   REVIEW.
RX   PubMed=9878383; DOI=10.1006/jmbi.1998.2354;
RA   Turner B.G., Summers M.F.;
RT   "Structural biology of HIV.";
RL   J. Mol. Biol. 285:1-32(1999).
RN   [4]
RP   REVIEW.
RX   PubMed=11700285; DOI=10.1146/annurev.genet.35.102401.090551;
RA   Negroni M., Buc H.;
RT   "Mechanisms of retroviral recombination.";
RL   Annu. Rev. Genet. 35:275-302(2001).
RN   [5]
RP   REVIEW.
RX   PubMed=11983066; DOI=10.1186/gb-2002-3-4-reviews3006;
RA   Dunn B.M., Goodenow M.M., Gustchina A., Wlodawer A.;
RT   "Retroviral proteases.";
RL   Genome Biol. 3:REVIEWS3006.1-REVIEWS3006.7(2002).
CC   -!- FUNCTION: [Gag-Pol polyprotein]: Mediates, with Gag polyprotein, the
CC       essential events in virion assembly, including binding the plasma
CC       membrane, making the protein-protein interactions necessary to create
CC       spherical particles, recruiting the viral Env proteins, and packaging
CC       the genomic RNA via direct interactions with the RNA packaging sequence
CC       (Psi). Gag-Pol polyprotein may regulate its own translation, by the
CC       binding genomic RNA in the 5'-UTR. At low concentration, the
CC       polyprotein would promote translation, whereas at high concentration,
CC       the polyprotein would encapsidate genomic RNA and then shut off
CC       translation. {ECO:0000250}.
CC   -!- FUNCTION: [Matrix protein p17]: Targets the polyprotein to the plasma
CC       membrane via a multipartite membrane-binding signal, that includes its
CC       myristoylated N-terminus. Matrix protein is part of the pre-integration
CC       complex. Implicated in the release from host cell mediated by Vpu.
CC       Binds to RNA. {ECO:0000250|UniProtKB:P12497}.
CC   -!- FUNCTION: [Capsid protein p24]: Forms the conical core that
CC       encapsulates the genomic RNA-nucleocapsid complex in the virion. Most
CC       core are conical, with only 7% tubular. The core is constituted by
CC       capsid protein hexamer subunits. The core is disassembled soon after
CC       virion entry (By similarity). Host restriction factors such as TRIM5-
CC       alpha or TRIMCyp bind retroviral capsids and cause premature capsid
CC       disassembly, leading to blocks in reverse transcription. Capsid
CC       restriction by TRIM5 is one of the factors which restricts HIV-1 to the
CC       human species. Host PIN1 apparently facilitates the virion uncoating.
CC       On the other hand, interactions with PDZD8 or CYPA stabilize the
CC       capsid. {ECO:0000250|UniProtKB:P04585, ECO:0000250|UniProtKB:P12497}.
CC   -!- FUNCTION: [Nucleocapsid protein p7]: Encapsulates and protects viral
CC       dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc
CC       fingers. Acts as a nucleic acid chaperone which is involved in
CC       rearangement of nucleic acid secondary structure during gRNA
CC       retrotranscription. Also facilitates template switch leading to
CC       recombination. As part of the polyprotein, participates in gRNA
CC       dimerization, packaging, tRNA incorporation and virion assembly.
CC       {ECO:0000250|UniProtKB:P04585}.
CC   -!- FUNCTION: [Protease]: Aspartyl protease that mediates proteolytic
CC       cleavages of Gag and Gag-Pol polyproteins during or shortly after the
CC       release of the virion from the plasma membrane. Cleavages take place as
CC       an ordered, step-wise cascade to yield mature proteins. This process is
CC       called maturation. Displays maximal activity during the budding process
CC       just prior to particle release from the cell. Also cleaves Nef and Vif,
CC       probably concomitantly with viral structural proteins on maturation of
CC       virus particles. Hydrolyzes host EIF4GI and PABP1 in order to shut off
CC       the capped cellular mRNA translation. The resulting inhibition of
CC       cellular protein synthesis serves to ensure maximal viral gene
CC       expression and to evade host immune response (By similarity).
CC       {ECO:0000250|UniProtKB:P04585, ECO:0000255|PROSITE-ProRule:PRU00275}.
CC   -!- FUNCTION: [Reverse transcriptase/ribonuclease H]: Multifunctional
CC       enzyme that converts the viral RNA genome into dsDNA in the cytoplasm,
CC       shortly after virus entry into the cell. This enzyme displays a DNA
CC       polymerase activity that can copy either DNA or RNA templates, and a
CC       ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-
CC       DNA heteroduplexes in a partially processive 3' to 5' endonucleasic
CC       mode. Conversion of viral genomic RNA into dsDNA requires many steps. A
CC       tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-
CC       end of the viral RNA. RT uses the 3' end of the tRNA primer to perform
CC       a short round of RNA-dependent minus-strand DNA synthesis. The reading
CC       proceeds through the U5 region and ends after the repeated (R) region
CC       which is present at both ends of viral RNA. The portion of the RNA-DNA
CC       heteroduplex is digested by the RNase H, resulting in a ssDNA product
CC       attached to the tRNA primer. This ssDNA/tRNA hybridizes with the
CC       identical R region situated at the 3' end of viral RNA. This template
CC       exchange, known as minus-strand DNA strong stop transfer, can be either
CC       intra- or intermolecular. RT uses the 3' end of this newly synthesized
CC       short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of
CC       the whole template. RNase H digests the RNA template except for two
CC       polypurine tracts (PPTs) situated at the 5'-end and near the center of
CC       the genome. It is not clear if both polymerase and RNase H activities
CC       are simultaneous. RNase H probably can proceed both in a polymerase-
CC       dependent (RNA cut into small fragments by the same RT performing DNA
CC       synthesis) and a polymerase-independent mode (cleavage of remaining RNA
CC       fragments by free RTs). Secondly, RT performs DNA-directed plus-strand
CC       DNA synthesis using the PPTs that have not been removed by RNase H as
CC       primers. PPTs and tRNA primers are then removed by RNase H. The 3' and
CC       5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate.
CC       Strand displacement synthesis by RT to the PBS and PPT ends produces a
CC       blunt ended, linear dsDNA copy of the viral genome that includes long
CC       terminal repeats (LTRs) at both ends. {ECO:0000250|UniProtKB:P04585}.
CC   -!- FUNCTION: [Integrase]: Catalyzes viral DNA integration into the host
CC       chromosome, by performing a series of DNA cutting and joining
CC       reactions. This enzyme activity takes place after virion entry into a
CC       cell and reverse transcription of the RNA genome in dsDNA. The first
CC       step in the integration process is 3' processing. This step requires a
CC       complex comprising the viral genome, matrix protein, Vpr and integrase.
CC       This complex is called the pre-integration complex (PIC). The integrase
CC       protein removes 2 nucleotides from each 3' end of the viral DNA,
CC       leaving recessed CA OH's at the 3' ends. In the second step, the PIC
CC       enters cell nucleus. This process is mediated through integrase and Vpr
CC       proteins, and allows the virus to infect a non dividing cell. This
CC       ability to enter the nucleus is specific of lentiviruses, other
CC       retroviruses cannot and rely on cell division to access cell
CC       chromosomes. In the third step, termed strand transfer, the integrase
CC       protein joins the previously processed 3' ends to the 5' ends of
CC       strands of target cellular DNA at the site of integration. The 5'-ends
CC       are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-
CC       shaped, gapped, recombination intermediate results, with the 5'-ends of
CC       the viral DNA strands and the 3' ends of target DNA strands remaining
CC       unjoined, flanking a gap of 5 bp. The last step is viral DNA
CC       integration into host chromosome. This involves host DNA repair
CC       synthesis in which the 5 bp gaps between the unjoined strands are
CC       filled in and then ligated. Since this process occurs at both cuts
CC       flanking the HIV genome, a 5 bp duplication of host DNA is produced at
CC       the ends of HIV-1 integration. Alternatively, Integrase may catalyze
CC       the excision of viral DNA just after strand transfer, this is termed
CC       disintegration. {ECO:0000250|UniProtKB:P04585}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endopeptidase for which the P1 residue is preferably
CC         hydrophobic.; EC=3.4.23.47; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU00275};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endohydrolysis of RNA in RNA/DNA hybrids. Three different
CC         cleavage modes: 1. sequence-specific internal cleavage of RNA. Human
CC         immunodeficiency virus type 1 and Moloney murine leukemia virus
CC         enzymes prefer to cleave the RNA strand one nucleotide away from the
CC         RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides
CC         from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides
CC         away from the primer terminus.; EC=3.1.26.13; Evidence={ECO:0000250};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=3'-end directed exonucleolytic cleavage of viral RNA-DNA
CC         hybrid.; EC=3.1.13.2; Evidence={ECO:0000250};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.49; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU00405};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.7; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU00405};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Binds 2 magnesium ions for reverse transcriptase polymerase
CC       activity. {ECO:0000250};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Binds 2 magnesium ions for ribonuclease H (RNase H) activity.
CC       Substrate-binding is a precondition for magnesium binding.
CC       {ECO:0000250};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Magnesium ions are required for integrase activity. Binds at least
CC       1, maybe 2 magnesium ions. {ECO:0000250};
CC   -!- ACTIVITY REGULATION: Protease: The viral protease is inhibited by many
CC       synthetic protease inhibitors (PIs), such as amprenavir, atazanavir,
CC       indinavir, loprinavir, nelfinavir, ritonavir and saquinavir. Use of
CC       protease inhibitors in tritherapy regimens permit more ambitious
CC       therapeutic strategies. Reverse transcriptase/ribonuclease H: RT can be
CC       inhibited either by nucleoside RT inhibitors (NRTIs) or by non
CC       nucleoside RT inhibitors (NNRTIs). NRTIs act as chain terminators,
CC       whereas NNRTIs inhibit DNA polymerization by binding a small
CC       hydrophobic pocket near the RT active site and inducing an allosteric
CC       change in this region. Classical NRTIs are abacavir, adefovir (PMEA),
CC       didanosine (ddI), lamivudine (3TC), stavudine (d4T), tenofovir (PMPA),
CC       zalcitabine (ddC), and zidovudine (AZT). Classical NNRTIs are
CC       atevirdine (BHAP U-87201E), delavirdine, efavirenz (DMP-266), emivirine
CC       (I-EBU), and nevirapine (BI-RG-587). The tritherapies used as a basic
CC       effective treatment of AIDS associate two NRTIs and one NNRTI.
CC       {ECO:0000250}.
CC   -!- SUBUNIT: [Matrix protein p17]: Homotrimer; further assembles as
CC       hexamers of trimers. Interacts with gp41 (via C-terminus). Interacts
CC       with host CALM1; this interaction induces a conformational change in
CC       the Matrix protein, triggering exposure of the myristate group.
CC       Interacts with host AP3D1; this interaction allows the polyprotein
CC       trafficking to multivesicular bodies during virus assembly. Part of the
CC       pre-integration complex (PIC) which is composed of viral genome, matrix
CC       protein, Vpr and integrase. {ECO:0000250|UniProtKB:P04591,
CC       ECO:0000250|UniProtKB:P12493}.
CC   -!- SUBUNIT: [Capsid protein p24]: Homodimer; the homodimer further
CC       multimerizes as homohexamers or homopentamers. Interacts with human
CC       PPIA/CYPA. Interacts with human NUP153. Interacts with host PDZD8; this
CC       interaction stabilizes the capsid. Interacts with monkey TRIM5; this
CC       interaction destabilizes the capsid. {ECO:0000250|UniProtKB:P03348,
CC       ECO:0000250|UniProtKB:P04591, ECO:0000250|UniProtKB:P12493}.
CC   -!- SUBUNIT: [Protease]: Homodimer, whose active site consists of two
CC       apposed aspartic acid residues. {ECO:0000250|UniProtKB:P04585,
CC       ECO:0000250|UniProtKB:P12497}.
CC   -!- SUBUNIT: [Reverse transcriptase/ribonuclease H]: Heterodimer of p66 RT
CC       and p51 RT (RT p66/p51) (By similarity). Heterodimerization of RT is
CC       essential for DNA polymerase activity (By similarity). The overall
CC       folding of the subdomains is similar in p66 RT and p51 RT but the
CC       spatial arrangements of the subdomains are dramatically different (By
CC       similarity). {ECO:0000250|UniProtKB:P03366}.
CC   -!- SUBUNIT: [Integrase]: Homotetramer; may further associate as a
CC       homohexadecamer (By similarity). Part of the pre-integration complex
CC       (PIC) which is composed of viral genome, matrix protein, Vpr and
CC       integrase. Interacts with human SMARCB1/INI1 and human PSIP1/LEDGF
CC       isoform 1. Interacts with human KPNA3; this interaction might play a
CC       role in nuclear import of the pre-integration complex (By similarity).
CC       Interacts with human NUP153; this interaction might play a role in
CC       nuclear import of the pre-integration complex (By similarity).
CC       {ECO:0000250|UniProtKB:P03367, ECO:0000250|UniProtKB:P04585,
CC       ECO:0000250|UniProtKB:P12497}.
CC   -!- SUBCELLULAR LOCATION: [Gag-Pol polyprotein]: Host cell membrane; Lipid-
CC       anchor. Host endosome, host multivesicular body. Note=These locations
CC       are linked to virus assembly sites. The main location is the cell
CC       membrane, but under some circumstances, late endosomal compartments can
CC       serve as productive sites for virion assembly.
CC       {ECO:0000250|UniProtKB:P12497}.
CC   -!- SUBCELLULAR LOCATION: [Matrix protein p17]: Virion membrane; Lipid-
CC       anchor {ECO:0000305}. Host nucleus {ECO:0000250}. Host cytoplasm
CC       {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: [Capsid protein p24]: Virion {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Nucleocapsid protein p7]: Virion {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Reverse transcriptase/ribonuclease H]: Virion
CC       {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Integrase]: Virion {ECO:0000305}. Host nucleus
CC       {ECO:0000305}. Host cytoplasm {ECO:0000305}. Note=Nuclear at initial
CC       phase, cytoplasmic at assembly. {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Ribosomal frameshifting; Named isoforms=2;
CC         Comment=Translation results in the formation of the Gag polyprotein
CC         most of the time. Ribosomal frameshifting at the gag-pol genes
CC         boundary occurs at low frequency and produces the Gag-Pol
CC         polyprotein. This strategy of translation probably allows the virus
CC         to modulate the quantity of each viral protein. Maintenance of a
CC         correct Gag to Gag-Pol ratio is essential for RNA dimerization and
CC         viral infectivity.;
CC       Name=Gag-Pol polyprotein;
CC         IsoId=P12451-1; Sequence=Displayed;
CC       Name=Gag polyprotein;
CC         IsoId=P12450-1; Sequence=External;
CC   -!- DOMAIN: [Reverse transcriptase/ribonuclease H]: RT is structured in
CC       five subdomains: finger, palm, thumb, connection and RNase H. Within
CC       the palm subdomain, the 'primer grip' region is thought to be involved
CC       in the positioning of the primer terminus for accommodating the
CC       incoming nucleotide. The RNase H domain stabilizes the association of
CC       RT with primer-template. {ECO:0000250}.
CC   -!- DOMAIN: [Reverse transcriptase/ribonuclease H]: The tryptophan repeat
CC       motif is involved in RT p66/p51 dimerization (By similarity).
CC       {ECO:0000250}.
CC   -!- DOMAIN: [Integrase]: The core domain contains the D-x(n)-D-x(35)-E
CC       motif, named for the phylogenetically conserved glutamic acid and
CC       aspartic acid residues and the invariant 35 amino acid spacing between
CC       the second and third acidic residues. Each acidic residue of the
CC       D,D(35)E motif is independently essential for the 3'-processing and
CC       strand transfer activities of purified integrase protein.
CC       {ECO:0000250}.
CC   -!- PTM: [Gag-Pol polyprotein]: Specific enzymatic cleavages by the viral
CC       protease yield mature proteins. The protease is released by
CC       autocatalytic cleavage. The polyprotein is cleaved during and after
CC       budding, this process is termed maturation. Proteolytic cleavage of p66
CC       RT removes the RNase H domain to yield the p51 RT subunit. Nucleocapsid
CC       protein p7 might be further cleaved after virus entry.
CC       {ECO:0000250|UniProtKB:P04585, ECO:0000255|PROSITE-ProRule:PRU00405}.
CC   -!- MISCELLANEOUS: [Reverse transcriptase/ribonuclease H]: Error-prone
CC       enzyme that lacks a proof-reading function. High mutations rate is a
CC       direct consequence of this characteristic. RT also displays frequent
CC       template switching leading to high recombination rate. Recombination
CC       mostly occurs between homologous regions of the two copackaged RNA
CC       genomes. If these two RNA molecules derive from different viral
CC       strains, reverse transcription will give rise to highly recombinated
CC       proviral DNAs. {ECO:0000250}.
CC   -!- MISCELLANEOUS: [Isoform Gag-Pol polyprotein]: Produced by -1 ribosomal
CC       frameshifting.
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DR   EMBL; J04498; AAB00746.1; ALT_SEQ; Genomic_DNA.
DR   SMR; P12451; -.
DR   MEROPS; A02.002; -.
DR   PRO; PR:P12451; -.
DR   Proteomes; UP000007427; Segment.
DR   GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0020002; C:host cell plasma membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0072494; C:host multivesicular body; IEA:UniProtKB-SubCell.
DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
DR   GO; GO:0019013; C:viral nucleocapsid; IEA:UniProtKB-KW.
DR   GO; GO:0055036; C:virion membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0004533; F:exoribonuclease H activity; IEA:UniProtKB-EC.
DR   GO; GO:0008289; F:lipid binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:InterPro.
DR   GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0039657; P:suppression by virus of host gene expression; IEA:UniProtKB-KW.
DR   GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
DR   GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
DR   GO; GO:0075732; P:viral penetration into host nucleus; IEA:UniProtKB-KW.
DR   CDD; cd05482; HIV_retropepsin_like; 1.
DR   Gene3D; 1.10.10.200; -; 1.
DR   Gene3D; 1.10.1200.30; -; 1.
DR   Gene3D; 3.30.70.270; -; 3.
DR   Gene3D; 2.40.70.10; Acid Proteases; 1.
DR   Gene3D; 3.10.10.10; HIV Type 1 Reverse Transcriptase, subunit A, domain 1; 1.
DR   Gene3D; 1.10.375.10; Human Immunodeficiency Virus Type 1 Capsid Protein; 1.
DR   Gene3D; 1.10.150.90; Immunodeficiency lentiviruses, gag gene matrix protein p17; 1.
DR   Gene3D; 2.30.30.10; Integrase, C-terminal domain superfamily, retroviral; 1.
DR   Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 2.
DR   Gene3D; 1.20.5.760; Single helix bin; 1.
DR   Gene3D; 4.10.60.10; Zinc finger, CCHC-type; 1.
DR   InterPro; IPR001969; Aspartic_peptidase_AS.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR045345; Gag_p24_C.
DR   InterPro; IPR017856; Integrase-like_N.
DR   InterPro; IPR036862; Integrase_C_dom_sf_retrovir.
DR   InterPro; IPR001037; Integrase_C_retrovir.
DR   InterPro; IPR001584; Integrase_cat-core.
DR   InterPro; IPR003308; Integrase_Zn-bd_dom_N.
DR   InterPro; IPR000071; Lentvrl_matrix_N.
DR   InterPro; IPR012344; Matrix_HIV/RSV_N.
DR   InterPro; IPR001995; Peptidase_A2_cat.
DR   InterPro; IPR021109; Peptidase_aspartic_dom_sf.
DR   InterPro; IPR034170; Retropepsin-like_cat_dom.
DR   InterPro; IPR018061; Retropepsins.
DR   InterPro; IPR008916; Retrov_capsid_C.
DR   InterPro; IPR008919; Retrov_capsid_N.
DR   InterPro; IPR010999; Retrovr_matrix.
DR   InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR002156; RNaseH_domain.
DR   InterPro; IPR036397; RNaseH_sf.
DR   InterPro; IPR000477; RT_dom.
DR   InterPro; IPR010659; RVT_connect.
DR   InterPro; IPR010661; RVT_thumb.
DR   InterPro; IPR001878; Znf_CCHC.
DR   InterPro; IPR036875; Znf_CCHC_sf.
DR   PANTHER; PTHR41694; ENDOGENOUS RETROVIRUS GROUP K MEMBER POL PROTEIN; 1.
DR   PANTHER; PTHR41694:SF3; RNA-DIRECTED DNA POLYMERASE-RELATED; 1.
DR   Pfam; PF00540; Gag_p17; 1.
DR   Pfam; PF00607; Gag_p24; 1.
DR   Pfam; PF19317; Gag_p24_C; 1.
DR   Pfam; PF00552; IN_DBD_C; 1.
DR   Pfam; PF02022; Integrase_Zn; 1.
DR   Pfam; PF00075; RNase_H; 1.
DR   Pfam; PF00665; rve; 1.
DR   Pfam; PF00077; RVP; 1.
DR   Pfam; PF00078; RVT_1; 1.
DR   Pfam; PF06815; RVT_connect; 1.
DR   Pfam; PF06817; RVT_thumb; 1.
DR   Pfam; PF00098; zf-CCHC; 2.
DR   PRINTS; PR00234; HIV1MATRIX.
DR   SMART; SM00343; ZnF_C2HC; 2.
DR   SUPFAM; SSF50630; Acid proteases; 1.
DR   SUPFAM; SSF50122; DNA-binding domain of retroviral integrase; 1.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   SUPFAM; SSF46919; N-terminal Zn binding domain of HIV integrase; 1.
DR   SUPFAM; SSF47836; Retroviral matrix proteins; 1.
DR   SUPFAM; SSF47353; Retrovirus capsid dimerization domain-like; 1.
DR   SUPFAM; SSF47943; Retrovirus capsid protein, N-terminal core domain; 1.
DR   SUPFAM; SSF57756; Retrovirus zinc finger-like domains; 1.
DR   SUPFAM; SSF53098; Ribonuclease H-like; 2.
DR   PROSITE; PS50175; ASP_PROT_RETROV; 1.
DR   PROSITE; PS00141; ASP_PROTEASE; 1.
DR   PROSITE; PS50994; INTEGRASE; 1.
DR   PROSITE; PS51027; INTEGRASE_DBD; 1.
DR   PROSITE; PS50879; RNASE_H_1; 1.
DR   PROSITE; PS50878; RT_POL; 1.
DR   PROSITE; PS50158; ZF_CCHC; 2.
DR   PROSITE; PS50876; ZF_INTEGRASE; 1.
PE   3: Inferred from homology;
KW   AIDS; Aspartyl protease; Capsid protein; DNA integration;
KW   DNA recombination; DNA-binding; DNA-directed DNA polymerase; Endonuclease;
KW   Eukaryotic host gene expression shutoff by virus;
KW   Eukaryotic host translation shutoff by virus; Host cell membrane;
KW   Host cytoplasm; Host endosome; Host gene expression shutoff by virus;
KW   Host membrane; Host nucleus; Host-virus interaction; Hydrolase;
KW   Lipid-binding; Lipoprotein; Magnesium; Membrane; Metal-binding;
KW   Multifunctional enzyme; Myristate; Nuclease; Nucleotidyltransferase;
KW   Protease; Repeat; Ribosomal frameshifting; RNA-binding;
KW   RNA-directed DNA polymerase; Transferase; Viral genome integration;
KW   Viral nucleoprotein; Viral penetration into host nucleus;
KW   Viral release from host cell; Virion; Virion maturation;
KW   Virus entry into host cell; Zinc; Zinc-finger.
FT   INIT_MET        1
FT                   /note="Removed; by host"
FT                   /evidence="ECO:0000250"
FT   CHAIN           2..1462
FT                   /note="Gag-Pol polyprotein"
FT                   /id="PRO_0000261299"
FT   CHAIN           2..135
FT                   /note="Matrix protein p17"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042515"
FT   CHAIN           136..364
FT                   /note="Capsid protein p24"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042516"
FT   PEPTIDE         365..381
FT                   /note="Spacer peptide 1"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042517"
FT   CHAIN           382..430
FT                   /note="Nucleocapsid protein p7"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042519"
FT   PEPTIDE         431..444
FT                   /note="Transframe peptide"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000246748"
FT   CHAIN           445..511
FT                   /note="p6-pol"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000042521"
FT   CHAIN           512..610
FT                   /note="Protease"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000038672"
FT   CHAIN           611..1169
FT                   /note="Reverse transcriptase/ribonuclease H"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042522"
FT   CHAIN           611..1049
FT                   /note="p51 RT"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042523"
FT   CHAIN           1050..1169
FT                   /note="p15"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042524"
FT   CHAIN           1170..1462
FT                   /note="Integrase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042525"
FT   DOMAIN          531..600
FT                   /note="Peptidase A2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00275"
FT   DOMAIN          654..844
FT                   /note="Reverse transcriptase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT   DOMAIN          1043..1166
FT                   /note="RNase H type-1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT   DOMAIN          1222..1373
FT                   /note="Integrase catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   ZN_FING         388..405
FT                   /note="CCHC-type 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT   ZN_FING         409..426
FT                   /note="CCHC-type 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT   ZN_FING         1172..1213
FT                   /note="Integrase-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT   DNA_BIND        1392..1439
FT                   /note="Integrase-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00506"
FT   REGION          7..31
FT                   /note="Interaction with Gp41"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          191..228
FT                   /note="Interaction with human PPIA/CYPA and NUP153"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          279..364
FT                   /note="Dimerization/Multimerization of capsid protein p24"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   REGION          441..507
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          512..516
FT                   /note="Dimerization of protease"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   REGION          560..566
FT                   /note="Dimerization of protease"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   REGION          599..611
FT                   /note="Dimerization of protease"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   REGION          837..845
FT                   /note="RT 'primer grip'"
FT                   /evidence="ECO:0000250"
FT   REGION          1443..1462
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           16..22
FT                   /note="Nuclear export signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           26..32
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           1007..1023
FT                   /note="Tryptophan repeat motif"
FT                   /evidence="ECO:0000250"
FT   COMPBIAS        450..467
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        471..506
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        536
FT                   /note="For protease activity; shared with dimeric partner"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10094"
FT   BINDING         720
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic; for reverse transcriptase
FT                   activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         795
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic; for reverse transcriptase
FT                   activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         796
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic; for reverse transcriptase
FT                   activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1052
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1087
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1107
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1158
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1181
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT   BINDING         1185
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT   BINDING         1209
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT   BINDING         1212
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT   BINDING         1233
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1285
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1321
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   SITE            135..136
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            222..223
FT                   /note="Cis/trans isomerization of proline peptide bond; by
FT                   human PPIA/CYPA"
FT                   /evidence="ECO:0000250"
FT   SITE            364..365
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            381..382
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            430..431
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000255"
FT   SITE            444..445
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            511..512
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            610..611
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            1010
FT                   /note="Essential for RT p66/p51 heterodimerization"
FT                   /evidence="ECO:0000250"
FT   SITE            1023
FT                   /note="Essential for RT p66/p51 heterodimerization"
FT                   /evidence="ECO:0000250"
FT   SITE            1049..1050
FT                   /note="Cleavage; by viral protease; partial"
FT                   /evidence="ECO:0000250"
FT   SITE            1169..1170
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   LIPID           2
FT                   /note="N-myristoyl glycine; by host"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1462 AA;  165014 MW;  DBA366324EA0167E CRC64;
     MGAKNSVLRG KKADELEKIR LRPGGKKKYR LKHIVWAANE LDRFGLTESL LESKEGCQKI
     ISVLEPLVPT GSENLKSLYN TTCVIWCLHA EEKVKDTEEA KRIVGRHLVA ETETAEKMPN
     ISRPTAPPSG KGGNFPVQQI GGNYVHLPLS PRTLNAWVKL VEEKKFGAEV VPGFQALSEG
     CTPYDINQML NCVGDHQAAM QIIREIINEE AADWDVQHPI PGPLPAGQLR DPRGSDIAGT
     TSTVEEQIEW MYRQENPVPV GNIYRRWIQI GLQKCVRMYN PTNILDIKQG PKESFQSYVD
     RFYKSLRAEQ TDAAVKNWMT QTLLVQSNPD CKLVLKGLGM NPTLEEMLTA CQGIGGPGQK
     ARLMAEALKE AMRPAPIPFA AAQQKRAIKC WNCGKEGHSA RQCRAPRRQG CWKCGKSGHI
     MANCPDRQAG FLRAWTMGKE APQLPRGPKF AGANTNSTPN GSSSGPTGEV HAAREKTERA
     ETKTIQRSDR GLAASRARRD TTQRDDRGLA APQFSLWKRP VVTAYIEDQP VEVLLDTGAD
     DSIVAGIELG SNYSPKIVGG IGGFINTKEY KDVEIRVLNK KVRATIMTGD TPINIFGRNI
     LTALGMSLNL PVAKIEPVKV TLKPGKDGPK QRQWPLTREK IEALREICEK MEREGQLEEA
     PPTNPYNTPT FAIKKKDKNK WRMLIDFREL NKVTQDFTEV QLGIPHPAGL AKKRRITVLD
     VGDAYFSIPL YEDFRQYTAF TLPSVNNAEP GKRYIYKVLP QGWKGSPAIF QYTMRQVLEP
     FRKANPDVII VQYMDDILIA SDRTDLEHDK VVLQLKELLN GLGFSTPDEK FQKDPPYQWM
     GYELWPTKWK LQKIQLPQKE VWTVNDIQKL VGVLNWAAQI YPGIKTKHLC KLIRGKMTPT
     EEVQWTELAE AELEENKIIL SQEQEGHYYQ EEKELEATVQ KDQDNQWTYK VHQGEKILKV
     GKYAKIKNTH TNGVRLLAQV VQKIGKEALV IWGRIPKFHL PVERETWEQW WDNYWQVTWI
     PDWDFVSTPP LVRLAFNLVK DPIPGAETFY TDGSCNRQSK EGKAGYITDR GKDKVRILEQ
     TTNQQAELEA FAMAVTDSGP KVNIVVDSQY VMGIVTGQPA ESESRIVNKI IEEMIKKEAI
     YVAWVPAHKG IGGNQEIDHL VSQGIRQVLF LERIEPAQEE HGKYHSNVKE LAHKFGLPNL
     VARQIVNTCA QCQQKGEAIH GQVNAELGTW QMDCTHLEGK IIIVAVHVAS GFIEAEVIPQ
     ESGRQTALFL LKLASRWPIT HLHTDNGANF TSQEVKMVAW WVGIEQSFGV PYNPQSQGVV
     EAMNHHLKNQ IERIREQANT METIVLMAVH CMNFKRRGGI GDMTPVERLV NMITTEQEIQ
     FLQAKNSKLK NFRVYFREGR NQLWQGPGEL LWKGDGAVIV KVGTDIKVIP RRKAKIIRDY
     GPRQEMDSGS HLEGAREDGE MA
//