POL_RSVP
ID POL_RSVP Reviewed; 1603 AA.
AC P03354; O92805; Q07462; Q64983;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 2.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Gag-Pol polyprotein;
DE Contains:
DE RecName: Full=Matrix protein p19;
DE Contains:
DE RecName: Full=p2A;
DE Contains:
DE RecName: Full=p2B;
DE Contains:
DE RecName: Full=p10;
DE Contains:
DE RecName: Full=Capsid protein p27, alternate cleaved 1;
DE Contains:
DE RecName: Full=Capsid protein p27, alternate cleaved 2;
DE Contains:
DE RecName: Full=Spacer peptide;
DE Short=SP;
DE AltName: Full=p3;
DE Contains:
DE RecName: Full=Nucleocapsid protein p12;
DE Contains:
DE RecName: Full=Protease p15;
DE EC=3.4.23.- {ECO:0000255|PROSITE-ProRule:PRU00275};
DE Contains:
DE RecName: Full=Reverse transcriptase beta-subunit;
DE Short=RT-beta;
DE Contains:
DE RecName: Full=Reverse transcriptase alpha-subunit;
DE Short=RT-alpha;
DE EC=2.7.7.49 {ECO:0000255|PROSITE-ProRule:PRU00405, ECO:0000269|PubMed:10708441};
DE EC=2.7.7.7 {ECO:0000255|PROSITE-ProRule:PRU00405, ECO:0000269|PubMed:10708441};
DE EC=3.1.26.4 {ECO:0000255|PROSITE-ProRule:PRU00408, ECO:0000269|PubMed:10708441};
DE Contains:
DE RecName: Full=Integrase;
DE Short=IN;
DE EC=2.7.7.- {ECO:0000269|PubMed:10669607, ECO:0000305|PubMed:11024025};
DE EC=3.1.-.- {ECO:0000269|PubMed:10669607, ECO:0000305|PubMed:11024025};
DE AltName: Full=pp32;
DE Contains:
DE RecName: Full=p4;
GN Name=gag-pol;
OS Rous sarcoma virus (strain Prague C) (RSV-PrC).
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Orthoretrovirinae; Alpharetrovirus.
OX NCBI_TaxID=11888;
OH NCBI_TaxID=9031; Gallus gallus (Chicken).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6299578; DOI=10.1016/0092-8674(83)90071-5;
RA Schwartz D., Tizard R., Gilbert W.;
RT "Nucleotide sequence of Rous sarcoma virus.";
RL Cell 32:853-869(1983).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=2982497; DOI=10.1016/0092-8674(85)90202-8;
RA Broome S., Gilbert W.;
RT "Rous sarcoma virus encodes a transcriptional activator.";
RL Cell 40:537-546(1985).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8387633;
RA Kashuba V.I., Kavsan V.M., Ryndich A.V., Lazurkevich Z.V., Zubak S.V.,
RA Popov S.V., Dostalova V., Glozhanek I.;
RT "Complete nucleotide sequence of Rous sarcoma virus variants adapted to
RT duck cells.";
RL Mol. Biol. (Mosk.) 27:436-450(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RA Chappey C.;
RL Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP PROTEOLYTIC PROCESSING (GAG-POL POLYPROTEIN).
RX PubMed=8636100; DOI=10.1074/jbc.271.12.6781;
RA Tozser J., Bagossi P., Weber I.T., Copeland T.D., Oroszlan S.;
RT "Comparative studies on the substrate specificity of avian myeloblastosis
RT virus proteinase and lentiviral proteinases.";
RL J. Biol. Chem. 271:6781-6788(1996).
RN [6]
RP RIBOSOMAL FRAMESHIFTING (GAG-POL POLYPROTEIN).
RX PubMed=9813113; DOI=10.1006/jmbi.1998.2186;
RA Marczinke B., Fisher R., Vidakovic M., Bloys A.J., Brierley I.;
RT "Secondary structure and mutational analysis of the ribosomal frameshift
RT signal of rous sarcoma virus.";
RL J. Mol. Biol. 284:205-225(1998).
RN [7]
RP SUBUNIT (REVERSE TRANSCRIPTASE ALPHA-SUBUNIT), SUBUNIT (REVERSE
RP TRANSCRIPTASE BETA-SUBUNIT), ACTIVE SITE (REVERSE TRANSCRIPTASE
RP ALPHA-SUBUNIT), CATALYTIC ACTIVITY (REVERSE TRANSCRIPTASE ALPHA-SUBUNIT),
RP AND MUTAGENESIS OF ASP-890 AND ASP-1213.
RX PubMed=10708441; DOI=10.1128/jvi.74.7.3245-3252.2000;
RA Werner S., Woehrl B.M.;
RT "Asymmetric subunit organization of heterodimeric Rous sarcoma virus
RT reverse transcriptase alphabeta: localization of the polymerase and RNase H
RT active sites in the alpha subunit.";
RL J. Virol. 74:3245-3252(2000).
RN [8]
RP FUNCTION (INTEGRASE), AND COFACTOR (INTEGRASE).
RX PubMed=11024025; DOI=10.1074/jbc.m007032200;
RA Skinner L.M., Sudol M., Harper A.L., Katzman M.;
RT "Nucleophile selection for the endonuclease activities of human, ovine, and
RT avian retroviral integrases.";
RL J. Biol. Chem. 276:114-124(2001).
RN [9]
RP PROTEOLYTIC CLEAVAGE (GAG-POL POLYPROTEIN).
RX PubMed=15102858; DOI=10.1074/jbc.m401868200;
RA Kadas J., Weber I.T., Bagossi P., Miklossy G., Boross P., Oroszlan S.,
RA Toezser J.;
RT "Narrow substrate specificity and sensitivity toward ligand-binding site
RT mutations of human T-cell Leukemia virus type 1 protease.";
RL J. Biol. Chem. 279:27148-27157(2004).
RN [10]
RP DOMAIN (GAG-POL POLYPROTEIN), AND MUTAGENESIS OF PRO-172 AND
RP 180-LEU--LEU-184.
RX PubMed=20392845; DOI=10.1128/jvi.00238-10;
RA Dilley K.A., Gregory D., Johnson M.C., Vogt V.M.;
RT "An LYPSL late domain in the gag protein contributes to the efficient
RT release and replication of Rous sarcoma virus.";
RL J. Virol. 84:6276-6287(2010).
RN [11]
RP REVIEW (INTEGRASE).
RX PubMed=28458055; DOI=10.1016/j.sbi.2017.04.005;
RA Engelman A.N., Cherepanov P.;
RT "Retroviral intasomes arising.";
RL Curr. Opin. Struct. Biol. 47:23-29(2017).
RN [12]
RP SUBUNIT (INTEGRASE).
RC STRAIN=Prague A;
RX PubMed=28184005; DOI=10.1074/jbc.m116.773382;
RA Pandey K.K., Bera S., Shi K., Aihara H., Grandgenett D.P.;
RT "A C-terminal 'tail' region in the Rous sarcoma virus integrase provides
RT high plasticity of functional integrase oligomerization during intasome
RT assembly.";
RL J. Biol. Chem. 292:5018-5030(2017).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 578-701 OF MUTANT SER-615;
RP ILE-619; ILE-621; MET-650; ALA-677; VAL-681; ARG-682; GLY-683; SER-684 WITH
RP INHIBITOR.
RC STRAIN=S9 variant;
RX PubMed=9521772; DOI=10.1021/bi972183g;
RA Wu J., Adomat J.M., Ridky T.W., Louis J.M., Leis J., Harrison R.W.,
RA Weber I.T.;
RT "Structural basis for specificity of retroviral proteases.";
RL Biochemistry 37:4518-4526(1998).
RN [14] {ECO:0007744|PDB:1C0M, ECO:0007744|PDB:1C1A}
RP X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS) OF 1329-1566, CATALYTIC ACTIVITY
RP (INTEGRASE), AND ACTIVE SITE (INTEGRASE).
RX PubMed=10669607; DOI=10.1006/jmbi.1999.3463;
RA Yang Z.N., Mueser T.C., Bushman F.D., Hyde C.C.;
RT "Crystal structure of an active two-domain derivative of Rous sarcoma virus
RT integrase.";
RL J. Mol. Biol. 296:535-548(2000).
RN [15] {ECO:0007744|PDB:3TIR}
RP X-RAY CRYSTALLOGRAPHY (4.10 ANGSTROMS) OF 240-465.
RX PubMed=22306463; DOI=10.1016/j.jmb.2012.01.014;
RA Bailey G.D., Hyun J.K., Mitra A.K., Kingston R.L.;
RT "A structural model for the generation of continuous curvature on the
RT surface of a retroviral capsid.";
RL J. Mol. Biol. 417:212-223(2012).
RN [16] {ECO:0007744|PDB:4FW1, ECO:0007744|PDB:4FW2}
RP X-RAY CRYSTALLOGRAPHY (1.86 ANGSTROMS) OF 1329-1550, AND SUBUNIT
RP (INTEGRASE).
RX PubMed=23451105; DOI=10.1371/journal.pone.0056892;
RA Shi K., Pandey K.K., Bera S., Vora A.C., Grandgenett D.P., Aihara H.;
RT "A possible role for the asymmetric C-terminal domain dimer of Rous sarcoma
RT virus integrase in viral DNA binding.";
RL PLoS ONE 8:E56892-E56892(2013).
RN [17] {ECO:0007744|PDB:5EJK}
RP X-RAY CRYSTALLOGRAPHY (3.80 ANGSTROMS) OF 1281-1550 IN COMPLEX WITH ZINC,
RP AND SUBUNIT (INTEGRASE).
RX PubMed=26887497; DOI=10.1038/nature16950;
RA Yin Z., Shi K., Banerjee S., Pandey K.K., Bera S., Grandgenett D.P.,
RA Aihara H.;
RT "Crystal structure of the Rous sarcoma virus intasome.";
RL Nature 530:362-366(2016).
CC -!- FUNCTION: Capsid protein p27: Self-associates to form the irregular
CC polyhedron core composed of hexamers and pentamers, that encapsulates
CC the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro.
CC {ECO:0000250|UniProtKB:P03322}.
CC -!- FUNCTION: [Spacer peptide]: Plays a role in the oligomerization of the
CC Gag polyprotein and in the stabilization of the immature particle.
CC Essential layering element during tube assembly.
CC {ECO:0000250|UniProtKB:P03322}.
CC -!- FUNCTION: [Nucleocapsid protein p12]: Binds strongly to viral nucleic
CC acids and promote their aggregation. Also destabilizes the nucleic
CC acids duplexes via highly structured zinc-binding motifs.
CC {ECO:0000305}.
CC -!- FUNCTION: [Protease p15]: The aspartyl protease 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. {ECO:0000255|PROSITE-
CC ProRule:PRU00275}.
CC -!- FUNCTION: [Integrase]: Catalyzes viral DNA integration into the host
CC chromosome, by performing a series of DNA cutting and joining
CC reactions. This recombination event is an essential step in the viral
CC replication cycle. Has a strong preference for using the 3'-OH at the
CC viral DNA end as a nucleophile. {ECO:0000269|PubMed:11024025}.
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 -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00408};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=The RT polymerase active site binds 2 magnesium ions.
CC {ECO:0000255|PROSITE-ProRule:PRU00405};
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;
CC Evidence={ECO:0000269|PubMed:10669607, ECO:0000269|PubMed:11024025};
CC Note=Binds 2 Mg(2+) ions per integrase homodimer. {ECO:0000250};
CC -!- SUBUNIT: [Protease p15]: Active as a homodimer (By similarity).
CC {ECO:0000250|UniProtKB:P03322}.
CC -!- SUBUNIT: [Integrase]: Homodimer; further associates as a homooctamer.
CC {ECO:0000250|UniProtKB:P03322, ECO:0000269|PubMed:23451105,
CC ECO:0000269|PubMed:26887497, ECO:0000269|PubMed:28184005,
CC ECO:0000303|PubMed:28458055}.
CC -!- SUBUNIT: [Reverse transcriptase beta-subunit]: Heterodimer of alpha and
CC beta subunits. Three forms of RT exist: alpha-alpha (alpha-Pol), beta-
CC beta (beta-Pol), and alpha-beta, with the major form being the
CC heterodimer. Both the polymerase and RNase H active sites are located
CC in the alpha subunit of heterodimeric RT alpha-beta.
CC {ECO:0000269|PubMed:10708441}.
CC -!- SUBUNIT: [Reverse transcriptase alpha-subunit]: Heterodimer of alpha
CC and beta subunits. Three forms of RT exist: alpha-alpha (alpha-Pol),
CC beta-beta (beta-Pol), and alpha-beta, with the major form being the
CC heterodimer. Both the polymerase and RNase H active sites are located
CC in the alpha subunit of heterodimeric RT alpha-beta.
CC {ECO:0000269|PubMed:10708441}.
CC -!- SUBCELLULAR LOCATION: [Matrix protein p19]: Virion {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein p27, alternate cleaved 1]: Virion
CC {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein p27, alternate cleaved 2]: Virion
CC {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Nucleocapsid protein p12]: Virion {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Ribosomal frameshifting; Named isoforms=2;
CC Comment=Translation results in the formation of the Gag polyprotein.
CC Ribosomal frameshifting at the gag/pol genes boundary produces the
CC Gag-Pol polyprotein. {ECO:0000269|PubMed:9813113};
CC Name=Gag-Pol polyprotein;
CC IsoId=P03354-1; Sequence=Displayed;
CC Name=Gag polyprotein;
CC IsoId=P03322-1; Sequence=External;
CC -!- DOMAIN: [Gag-Pol polyprotein]: Late-budding domains (L domains) are
CC short sequence motifs essential for viral particle release. They can
CC occur individually or in close proximity within structural proteins.
CC They interacts with sorting cellular proteins of the multivesicular
CC body (MVB) pathway. Most of these proteins are class E vacuolar protein
CC sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes.
CC P2B contains two L domain: a PPXY motif which probably binds to the WW
CC domains of HECT (homologous to E6-AP C-terminus) E3 ubiquitin ligases
CC and a LYPX(n)L domain which is known to bind the Alix adaptator
CC protein. {ECO:0000269|PubMed:20392845}.
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 (By
CC similarity). {ECO:0000250}.
CC -!- DOMAIN: [Gag-Pol polyprotein]: Contains a nuclear export signal in p10
CC and a nucleolar localization signal in nucleocapsid protein p12.
CC {ECO:0000250|UniProtKB:P03322}.
CC -!- DOMAIN: Capsid protein p27: Proton-driven dimerization of the C-
CC terminus facilitates capsid assembly. {ECO:0000250|UniProtKB:P03322}.
CC -!- PTM: [Isoform Gag-Pol polyprotein]: Specific enzymatic cleavages in
CC vivo yield mature proteins. {ECO:0000269|PubMed:15102858,
CC ECO:0000269|PubMed:8636100}.
CC -!- PTM: Capsid protein p27: The cleavage at the C-terminus is slowly
CC trimmed by the viral protease, sometimes being cut internally thereby
CC generating the short version of the capsid protein and a capsid protein
CC C-terminally extended by 3 amino acids in a ratio of 2:1.
CC {ECO:0000250|UniProtKB:P03322}.
CC -!- MISCELLANEOUS: Reverse transcriptase: Error-prone enzyme that lacks a
CC proof-reading function. High mutations rate is a direct consequence of
CC this characteristic. RT also displays frequent template switching
CC leading to high recombination rate. Recombination mostly occurs between
CC homologous regions of the two copackaged RNA genomes. If these two RNA
CC molecules derive from different viral strains, reverse transcription
CC will give rise to highly recombinated proviral DNAs.
CC {ECO:0000255|PROSITE-ProRule:PRU00405}.
CC -!- MISCELLANEOUS: [Isoform Gag-Pol polyprotein]: Produced by -1 ribosomal
CC frameshifting. {ECO:0000269|PubMed:9813113}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB59933.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; V01197; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; J02342; AAB59933.1; ALT_INIT; Genomic_RNA.
DR EMBL; X68524; CAA48535.1; -; Genomic_DNA.
DR EMBL; AF033808; AAC82561.1; -; Genomic_RNA.
DR PIR; A03955; GNFV1R.
DR RefSeq; NP_056886.1; NC_001407.1.
DR PDB; 1BAI; X-ray; 2.40 A; A/B=578-701.
DR PDB; 1C0M; X-ray; 2.53 A; A/B/C/D=1329-1566.
DR PDB; 1C1A; X-ray; 3.10 A; A/B=1329-1566.
DR PDB; 3TIR; X-ray; 4.10 A; A=240-465.
DR PDB; 4FW1; X-ray; 1.86 A; A/B=1329-1550.
DR PDB; 4FW2; X-ray; 2.65 A; A/B=1281-1550.
DR PDB; 5EJK; X-ray; 3.80 A; A/B/C/D/E/F/G/H=1281-1550.
DR PDB; 5KZ9; X-ray; 2.85 A; A=1-155.
DR PDB; 5KZA; X-ray; 1.86 A; A=2-102.
DR PDB; 5KZB; X-ray; 3.20 A; A=2-102.
DR PDB; 6CCJ; NMR; -; A=2-87.
DR PDB; 6CE5; NMR; -; A=2-87.
DR PDB; 6CUS; NMR; -; A=2-87.
DR PDB; 6CV8; NMR; -; A=2-87.
DR PDB; 6CW4; NMR; -; A=2-87.
DR PDB; 7JN3; EM; 3.21 A; A/B/C/D/E/F/G/H=1281-1558.
DR PDB; 7KU7; EM; 3.40 A; A/B/C/D/E/F/G/H=1281-1558.
DR PDB; 7KUI; EM; 3.40 A; A/B/C/D/E/F/G/H=1281-1558.
DR PDBsum; 1BAI; -.
DR PDBsum; 1C0M; -.
DR PDBsum; 1C1A; -.
DR PDBsum; 3TIR; -.
DR PDBsum; 4FW1; -.
DR PDBsum; 4FW2; -.
DR PDBsum; 5EJK; -.
DR PDBsum; 5KZ9; -.
DR PDBsum; 5KZA; -.
DR PDBsum; 5KZB; -.
DR PDBsum; 6CCJ; -.
DR PDBsum; 6CE5; -.
DR PDBsum; 6CUS; -.
DR PDBsum; 6CV8; -.
DR PDBsum; 6CW4; -.
DR PDBsum; 7JN3; -.
DR PDBsum; 7KU7; -.
DR PDBsum; 7KUI; -.
DR BMRB; P03354; -.
DR SMR; P03354; -.
DR BindingDB; P03354; -.
DR ChEMBL; CHEMBL2750; -.
DR MEROPS; A02.015; -.
DR GeneID; 2193432; -.
DR KEGG; vg:2193432; -.
DR EvolutionaryTrace; P03354; -.
DR Proteomes; UP000007183; Genome.
DR Proteomes; UP000137552; Genome.
DR GO; GO:0019013; C:viral nucleocapsid; IEA:UniProtKB-KW.
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: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:UniProtKB-EC.
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:0001171; P:reverse transcription; IDA:UniProtKB.
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 CDD; cd05482; HIV_retropepsin_like; 1.
DR Gene3D; 1.10.10.200; -; 1.
DR Gene3D; 1.10.1200.30; -; 1.
DR Gene3D; 1.10.150.90; -; 1.
DR Gene3D; 1.10.375.10; -; 1.
DR Gene3D; 2.30.30.10; -; 1.
DR Gene3D; 2.40.70.10; -; 1.
DR Gene3D; 3.30.420.10; -; 2.
DR Gene3D; 3.30.70.270; -; 2.
DR InterPro; IPR001969; Aspartic_peptidase_AS.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR004028; Gag_M.
DR InterPro; IPR000721; Gag_p24_N.
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; 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; IPR010661; RVT_thumb.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR Pfam; PF00607; Gag_p24; 1.
DR Pfam; PF00552; IN_DBD_C; 1.
DR Pfam; PF02022; Integrase_Zn; 1.
DR Pfam; PF02813; Retro_M; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF00077; RVP; 1.
DR Pfam; PF00078; RVT_1; 1.
DR Pfam; PF06817; RVT_thumb; 1.
DR Pfam; PF00098; zf-CCHC; 1.
DR SMART; SM00343; ZnF_C2HC; 2.
DR SUPFAM; SSF46919; SSF46919; 1.
DR SUPFAM; SSF47836; SSF47836; 1.
DR SUPFAM; SSF47943; SSF47943; 1.
DR SUPFAM; SSF50122; SSF50122; 1.
DR SUPFAM; SSF50630; SSF50630; 1.
DR SUPFAM; SSF53098; SSF53098; 2.
DR SUPFAM; SSF56672; SSF56672; 1.
DR SUPFAM; SSF57756; SSF57756; 1.
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; 1.
DR PROSITE; PS50876; ZF_INTEGRASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aspartyl protease; Capsid protein; DNA integration;
KW DNA recombination; DNA-binding; DNA-directed DNA polymerase; Endonuclease;
KW Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotidyltransferase; Protease; Repeat; Ribosomal frameshifting;
KW RNA-binding; RNA-directed DNA polymerase; Transferase;
KW Viral genome integration; Viral nucleoprotein; Virion;
KW Virus entry into host cell; Zinc; Zinc-finger.
FT CHAIN 1..1603
FT /note="Gag-Pol polyprotein"
FT /id="PRO_0000442482"
FT CHAIN 1..155
FT /note="Matrix protein p19"
FT /id="PRO_5000053588"
FT CHAIN 156..166
FT /note="p2A"
FT /id="PRO_0000397068"
FT CHAIN 167..177
FT /note="p2B"
FT /id="PRO_0000397069"
FT CHAIN 178..239
FT /note="p10"
FT /id="PRO_5000053589"
FT CHAIN 240..479
FT /note="Capsid protein p27, alternate cleaved 2"
FT /id="PRO_5000053590"
FT CHAIN 240..476
FT /note="Capsid protein p27, alternate cleaved 1"
FT /id="PRO_0000442483"
FT PEPTIDE 480..488
FT /note="Spacer peptide"
FT /id="PRO_0000397070"
FT CHAIN 489..577
FT /note="Nucleocapsid protein p12"
FT /id="PRO_5000053591"
FT CHAIN 578..708
FT /note="Protease p15"
FT /id="PRO_5000053592"
FT CHAIN 709..1567
FT /note="Reverse transcriptase beta-subunit"
FT /id="PRO_0000397071"
FT CHAIN 709..1280
FT /note="Reverse transcriptase alpha-subunit"
FT /id="PRO_0000040986"
FT CHAIN 1281..1567
FT /note="Integrase"
FT /id="PRO_0000040987"
FT CHAIN 1568..1603
FT /note="p4"
FT /id="PRO_0000397072"
FT DOMAIN 609..690
FT /note="Peptidase A2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00275"
FT DOMAIN 750..938
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT DOMAIN 1149..1280
FT /note="RNase H type-1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT DOMAIN 1333..1496
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT ZN_FING 507..524
FT /note="CCHC-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT ZN_FING 533..550
FT /note="CCHC-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT ZN_FING 1280..1321
FT /note="Integrase-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT DNA_BIND 1502..1550
FT /note="Integrase-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00506"
FT REGION 128..150
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 181..217
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 217..259
FT /note="Involved in capsid protein dimerization"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT REGION 290..298
FT /note="Involved in capsid protein dimerization"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT REGION 351..362
FT /note="Involved in capsid protein dimerization"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT REGION 543..575
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1548..1567
FT /note="Involved in homooctamerization"
FT /evidence="ECO:0000269|PubMed:28184005"
FT REGION 1569..1603
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 172..175
FT /note="PPXY motif"
FT /evidence="ECO:0000269|PubMed:20392845"
FT MOTIF 180..184
FT /note="LYPX(n)L motif"
FT /evidence="ECO:0000269|PubMed:20392845"
FT MOTIF 219..229
FT /note="Nuclear export signal"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT MOTIF 524..527
FT /note="Nuclear/nucleolar localization signal"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT COMPBIAS 1589..1603
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 614
FT /note="For protease activity; shared with dimeric partner"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10094"
FT BINDING 815
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:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 890
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:0000269|PubMed:10708441"
FT BINDING 891
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:0000255|PROSITE-ProRule:PRU00405"
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:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 1192
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:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 1213
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:0000255|PROSITE-ProRule:PRU00405,
FT ECO:0000269|PubMed:10708441"
FT BINDING 1272
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:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 1289
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 1293
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 1317
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 1320
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 1344
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405,
FT ECO:0000269|PubMed:10669607"
FT BINDING 1401
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405,
FT ECO:0000269|PubMed:10669607"
FT BINDING 1437
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for integrase activity"
FT /evidence="ECO:0000269|PubMed:10669607"
FT SITE 155..156
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 166..167
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 177..178
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 239..240
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 418
FT /note="Involved in capsid protein dimerization upon
FT acidification"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 430
FT /note="Involved in capsid protein dimerization upon
FT acidification"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 476..477
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 479..480
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 488..489
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 577..578
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000250|UniProtKB:P03322"
FT SITE 708..709
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000303|PubMed:15102858"
FT SITE 1280..1281
FT /note="Cleavage; by viral protease p15"
FT /evidence="ECO:0000303|PubMed:15102858"
FT SITE 1567..1568
FT /note="Cleavage; by viral protease p15"
FT VARIANT 722
FT /note="P -> S"
FT VARIANT 724
FT /note="H -> R"
FT VARIANT 884
FT /note="C -> R"
FT VARIANT 907
FT /note="E -> K"
FT VARIANT 955
FT /note="A -> T"
FT VARIANT 1012
FT /note="R -> Q"
FT VARIANT 1182
FT /note="A -> V"
FT VARIANT 1243
FT /note="S -> G"
FT VARIANT 1575
FT /note="E -> G"
FT VARIANT 1577
FT /note="E -> K"
FT MUTAGEN 172
FT /note="P->A: 75% loss of budding."
FT /evidence="ECO:0000269|PubMed:20392845"
FT MUTAGEN 180..184
FT /note="LYPSL->AAASA: 40% loss of budding."
FT /evidence="ECO:0000269|PubMed:20392845"
FT MUTAGEN 890
FT /note="D->N: 58% loss of polymerase activity when the
FT mutation targets the reverse transcriptase beta subunit;
FT 93% loss of polymerase activity when the mutation targets
FT the reverse transcriptase alpha-subunit."
FT /evidence="ECO:0000269|PubMed:10708441"
FT MUTAGEN 1213
FT /note="D->N: 26% loss of polymerase activity when the
FT mutation targets the reverse transcriptase beta subunit;
FT 56% loss of polymerase activity when the mutation targets
FT the reverse transcriptase alpha-subunit."
FT /evidence="ECO:0000269|PubMed:10708441"
FT CONFLICT 756
FT /note="E -> V (in Ref. 3; CAA48535)"
FT /evidence="ECO:0000305"
FT CONFLICT 1206
FT /note="T -> A (in Ref. 3; CAA48535)"
FT /evidence="ECO:0000305"
FT CONFLICT 1274
FT /note="Q -> K (in Ref. 3; CAA48535)"
FT /evidence="ECO:0000305"
FT CONFLICT 1381
FT /note="V -> A (in Ref. 3; CAA48535)"
FT /evidence="ECO:0000305"
FT HELIX 2..15
FT /evidence="ECO:0007829|PDB:5KZA"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:5KZ9"
FT HELIX 23..35
FT /evidence="ECO:0007829|PDB:5KZA"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:6CE5"
FT HELIX 42..46
FT /evidence="ECO:0007829|PDB:5KZA"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:5KZA"
FT HELIX 51..65
FT /evidence="ECO:0007829|PDB:5KZA"
FT HELIX 69..91
FT /evidence="ECO:0007829|PDB:5KZA"
FT HELIX 1283..1292
FT /evidence="ECO:0007829|PDB:7JN3"
FT HELIX 1296..1302
FT /evidence="ECO:0007829|PDB:7JN3"
FT HELIX 1307..1314
FT /evidence="ECO:0007829|PDB:7JN3"
FT HELIX 1318..1320
FT /evidence="ECO:0007829|PDB:7JN3"
FT STRAND 1321..1324
FT /evidence="ECO:0007829|PDB:7JN3"
FT STRAND 1339..1347
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1349..1351
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1356..1362
FT /evidence="ECO:0007829|PDB:4FW1"
FT TURN 1363..1365
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1368..1375
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1378..1392
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1396..1400
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1404..1407
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1409..1418
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1421..1424
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1430..1433
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1435..1453
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1457..1459
FT /evidence="ECO:0007829|PDB:1C0M"
FT HELIX 1462..1464
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1465..1478
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1488..1493
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1503..1507
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1509..1511
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1513..1522
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1524..1531
FT /evidence="ECO:0007829|PDB:4FW1"
FT TURN 1532..1534
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1537..1541
FT /evidence="ECO:0007829|PDB:4FW1"
FT HELIX 1542..1544
FT /evidence="ECO:0007829|PDB:4FW1"
FT STRAND 1545..1547
FT /evidence="ECO:0007829|PDB:4FW1"
SQ SEQUENCE 1603 AA; 173881 MW; 01AF800FDF929CB6 CRC64;
MEAVIKVISS ACKTYCGKTS PSKKEIGAML SLLQKEGLLM SPSDLYSPGS WDPITAALSQ
RAMILGKSGE LKTWGLVLGA LKAAREEQVT SEQAKFWLGL GGGRVSPPGP ECIEKPATER
RIDKGEEVGE TTVQRDAKMA PEETATPKTV GTSCYHCGTA IGCNCATASA PPPPYVGSGL
YPSLAGVGEQ QGQGGDTPPG AEQSRAEPGH AGQAPGPALT DWARVREELA STGPPVVAMP
VVIKTEGPAW TPLEPKLITR LADTVRTKGL RSPITMAEVE ALMSSPLLPH DVTNLMRVIL
GPAPYALWMD AWGVQLQTVI AAATRDPRHP ANGQGRGERT NLNRLKGLAD GMVGNPQGQA
ALLRPGELVA ITASALQAFR EVARLAEPAG PWADIMQGPS ESFVDFANRL IKAVEGSDLP
PSARAPVIID CFRQKSQPDI QQLIRTAPST LTTPGEIIKY VLDRQKTAPL TDQGIAAAMS
SAIQPLIMAV VNRERDGQTG SGGRARGLCY TCGSPGHYQA QCPKKRKSGN SRERCQLCNG
MGHNAKQCRK RDGNQGQRPG KGLSSGPWPG PEPPAVSLAM TMEHKDRPLV RVILTNTGSH
PVKQRSVYIT ALLDSGADIT IISEEDWPTD WPVMEAANPQ IHGIGGGIPM RKSRDMIELG
VINRDGSLER PLLLFPAVAM VRGSILGRDC LQGLGLRLTN LIGRATVLTV ALHLAIPLKW
KPDHTPVWID QWPLPEGKLV ALTQLVEKEL QLGHIEPSLS CWNTPVFVIR KASGSYRLLH
DLRAVNAKLV PFGAVQQGAP VLSALPRGWP LMVLDLKDCF FSIPLAEQDR EAFAFTLPSV
NNQAPARRFQ WKVLPQGMTC SPTICQLVVG QVLEPLRLKH PSLCMLHYMD DLLLAASSHD
GLEAAGEEVI STLERAGFTI SPDKVQREPG VQYLGYKLGS TYVAPVGLVA EPRIATLWDV
QKLVGSLQWL RPALGIPPRL MGPFYEQLRG SDPNEAREWN LDMKMAWREI VRLSTTAALE
RWDPALPLEG AVARCEQGAI GVLGQGLSTH PRPCLWLFST QPTKAFTAWL EVLTLLITKL
RASAVRTFGK EVDILLLPAC FREDLPLPEG ILLALKGFAG KIRSSDTPSI FDIARPLHVS
LKVRVTDHPV PGPTVFTDAS SSTHKGVVVW REGPRWEIKE IADLGASVQQ LEARAVAMAL
LLWPTTPTNV VTDSAFVAKM LLKMGQEGVP STAAAFILED ALSQRSAMAA VLHVRSHSEV
PGFFTEGNDV ADSQATFQAY PLREAKDLHT ALHIGPRALS KACNISMQQA REVVQTCPHC
NSAPALEAGV NPRGLGPLQI WQTDFTLEPR MAPRSWLAVT VDTASSAIVV TQHGRVTSVA
VQHHWATAIA VLGRPKAIKT DNGSCFTSKS TREWLARWGI AHTTGIPGNS QGQAMVERAN
RLLKDRIRVL AEGDGFMKRI PTSKQGELLA KAMYALNHFE RGENTKTPIQ KHWRPTVLTE
GPPVKIRIET GEWEKGWNVL VWGRGYAAVK NRDTDKVIWV PSRKVKPDIT QKDEVTKKDE
ASPLFAGISD WIPWEDEQEG LQGETASNKQ ERPGEDTLAA NES
