ID   POL_XMRV3               Reviewed;        1733 AA.
AC   Q2F7J3;
DT   19-JAN-2010, integrated into UniProtKB/Swiss-Prot.
DT   21-MAR-2006, sequence version 1.
DT   27-MAR-2024, entry version 110.
DE   RecName: Full=Gag-Pol polyprotein;
DE            Short=Pr180gag-pol;
DE   Contains:
DE     RecName: Full=Matrix protein p15;
DE              Short=MA;
DE   Contains:
DE     RecName: Full=RNA-binding phosphoprotein p12;
DE     AltName: Full=pp12;
DE   Contains:
DE     RecName: Full=Capsid protein p30;
DE              Short=CA;
DE   Contains:
DE     RecName: Full=Nucleocapsid protein p10;
DE              Short=NC-pol;
DE   Contains:
DE     RecName: Full=Protease p14;
DE              Short=PR;
DE              EC=3.4.23.-;
DE   Contains:
DE     RecName: Full=Reverse transcriptase/ribonuclease H p80;
DE              Short=RT;
DE              EC=2.7.7.49;
DE              EC=2.7.7.7;
DE              EC=3.1.26.4;
DE   Contains:
DE     RecName: Full=Integrase p46;
DE              Short=IN;
DE              EC=2.7.7.- {ECO:0000250|UniProtKB:P03355};
DE              EC=3.1.-.- {ECO:0000250|UniProtKB:P03355};
GN   Name=gag-pol;
OS   Xenotropic MuLV-related virus (isolate VP35) (XMRV).
OC   Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC   Ortervirales; Retroviridae; Orthoretrovirinae; Gammaretrovirus;
OC   Murine leukemia-related retroviruses.
OX   NCBI_TaxID=356663;
OH   NCBI_TaxID=9606; Homo sapiens (Human).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA], AND RETRACTED PAPER.
RX   PubMed=16609730; DOI=10.1371/journal.ppat.0020025;
RA   Urisman A., Molinaro R.J., Fischer N., Plummer S.J., Casey G., Klein E.A.,
RA   Malathi K., Magi-Galluzzi C., Tubbs R.R., Ganem D., Silverman R.H.,
RA   DeRisi J.L.;
RT   "Identification of a novel Gammaretrovirus in prostate tumors of patients
RT   homozygous for R462Q RNASEL variant.";
RL   PLoS Pathog. 2:E25-E25(2006).
RN   [2]
RP   RETRACTION NOTICE OF PUBMED:16609730.
RX   PubMed=23028303;
RX   DOI=10.1371/annotation/7e2efc01-2e9b-4e9b-aef0-87ab0e4e4732;
RA   Urisman A., Molinaro R.J., Fischer N., Plummer S.J., Casey G., Klein E.A.,
RA   Malathi K., Magi-Galluzzi C., Tubbs R.R., Ganem D., Silverman R.H.,
RA   DeRisi J.L.;
RL   PLoS Pathog. 8:0-0(2012).
RN   [3] {ECO:0007744|PDB:3V1O, ECO:0007744|PDB:3V1Q, ECO:0007744|PDB:3V1R}
RP   X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) OF 1154-1328 IN COMPLEX WITH MN(2+)
RP   AND BETA-THUJAPLICINOL, AND COFACTOR (REVERSE TRANSCRIPTASE/RIBONUCLEASE H
RP   P80).
RX   PubMed=22366278; DOI=10.1016/j.jsb.2012.02.006;
RA   Zhou D., Chung S., Miller M., Grice S.F., Wlodawer A.;
RT   "Crystal structures of the reverse transcriptase-associated ribonuclease H
RT   domain of xenotropic murine leukemia-virus related virus.";
RL   J. Struct. Biol. 177:638-645(2012).
CC   -!- FUNCTION: [Gag-Pol polyprotein]: Plays a role in budding and is
CC       processed by the viral protease during virion maturation outside the
CC       cell. During budding, it recruits, in a PPXY-dependent or independent
CC       manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules
CC       to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin
CC       ligases probably link the viral protein to the host ESCRT pathway and
CC       facilitate release. {ECO:0000250|UniProtKB:P03332}.
CC   -!- FUNCTION: [Matrix protein p15]: Targets Gag and gag-pol polyproteins to
CC       the plasma membrane via a multipartite membrane binding signal, that
CC       includes its myristoylated N-terminus. Also mediates nuclear
CC       localization of the pre-integration complex.
CC       {ECO:0000250|UniProtKB:P03332}.
CC   -!- FUNCTION: [Capsid protein p30]: Forms the spherical core of the virion
CC       that encapsulates the genomic RNA-nucleocapsid complex.
CC       {ECO:0000250|UniProtKB:P03336}.
CC   -!- FUNCTION: [Nucleocapsid protein p10]: Involved in the packaging and
CC       encapsidation of two copies of the genome (By similarity). Binds with
CC       high affinity to conserved UCUG elements within the packaging signal,
CC       located near the 5'-end of the genome (By similarity). This binding is
CC       dependent on genome dimerization (By similarity). Acts as a nucleic
CC       acid chaperone which is involved in rearrangement of nucleic acid
CC       secondary structures during gRNA retrotranscription (By similarity).
CC       {ECO:0000250|UniProtKB:P03332, ECO:0000250|UniProtKB:P03355}.
CC   -!- FUNCTION: [Protease p14]: 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: [Reverse transcriptase/ribonuclease H p80]: RT is a
CC       multifunctional enzyme that converts the viral dimeric RNA genome into
CC       dsDNA in the cytoplasm, shortly after virus entry into the cell. This
CC       enzyme displays a DNA polymerase activity that can copy either DNA or
CC       RNA templates, and a ribonuclease H (RNase H) activity that cleaves the
CC       RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5'
CC       endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires
CC       many steps. A tRNA binds to the primer-binding site (PBS) situated at
CC       the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to
CC       perform a short round of RNA-dependent minus-strand DNA synthesis. The
CC       reading proceeds through the U5 region and ends after the repeated (R)
CC       region which is present at both ends of viral RNA. The portion of the
CC       RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA
CC       product attached to the tRNA primer. This ssDNA/tRNA hybridizes with
CC       the identical R region situated at the 3' end of viral RNA. This
CC       template exchange, known as minus-strand DNA strong stop transfer, can
CC       be either intra- or intermolecular. RT uses the 3' end of this newly
CC       synthesized short ssDNA to perform the RNA-dependent minus-strand DNA
CC       synthesis of the whole template. RNase H digests the RNA template
CC       except for a polypurine tract (PPT) situated at the 5' end of the
CC       genome. It is not clear if both polymerase and RNase H activities are
CC       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 PPT that has not been removed by RNase H as
CC       primers. PPT 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 (By similarity). {ECO:0000250}.
CC   -!- FUNCTION: [Integrase p46]: Catalyzes viral DNA integration into the
CC       host 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 and integrase. This
CC       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 that
CC       requires cell division, the PIC enters cell nucleus. In the third step,
CC       termed strand transfer, the integrase protein joins the previously
CC       processed 3' ends to the 5' ends of strands of target cellular DNA at
CC       the site of integration. The last step is viral DNA integration into
CC       host chromosome. {ECO:0000250|UniProtKB:P03355}.
CC   -!- CATALYTIC ACTIVITY: [Reverse transcriptase/ribonuclease H p80]:
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: [Reverse transcriptase/ribonuclease H p80]:
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: [Protease p14]:
CC       Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00408};
CC   -!- COFACTOR: [Reverse transcriptase/ribonuclease H p80]:
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: [Reverse transcriptase/ribonuclease H p80]:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:22366278};
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000250|UniProtKB:A1Z651};
CC       Note=Binds 2 Mn(2+)/Mg(2+) ions for ribonuclease H (RNase H) activity
CC       (PubMed:22366278). Shows 4- to 6-fold increased rates of cleavage in
CC       the presence of Mn(2+) versus Mg2(2+) (By similarity).
CC       {ECO:0000250|UniProtKB:A1Z651, ECO:0000269|PubMed:22366278};
CC   -!- COFACTOR: [Integrase p46]:
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   -!- SUBUNIT: [Capsid protein p30]: Homohexamer, that further associates as
CC       homomultimer. The virus core is composed of a lattice formed from
CC       hexagonal rings, each containing six capsid monomers. The protease is a
CC       homodimer, whose active site consists of two apposed aspartic acid
CC       residues. The reverse transcriptase is a monomer.
CC       {ECO:0000250|UniProtKB:P03355}.
CC   -!- SUBUNIT: [Gag-Pol polyprotein]: Interacts (via PPXY motif) with host
CC       NEDD4 (By similarity). Interacts (via PSAP motif) with host TSG101 (By
CC       similarity). Interacts (via LYPX(n)L motif) with host PDCD6IP (By
CC       similarity). {ECO:0000250|UniProtKB:P03355}.
CC   -!- SUBUNIT: [Reverse transcriptase/ribonuclease H p80]: The reverse
CC       transcriptase is a monomer (Potential). Interacts (via RNase domains)
CC       with host release factor ETF1; this interaction is essential for
CC       translational readthrough of amber codon between viral gag and pol
CC       genes, as well as for viral replication.
CC       {ECO:0000250|UniProtKB:P03355}.
CC   -!- SUBUNIT: [Integrase p46]: Homodimer. {ECO:0000250|UniProtKB:P03355}.
CC   -!- SUBCELLULAR LOCATION: [Gag-Pol polyprotein]: Host cell membrane
CC       {ECO:0000305}; Lipid-anchor {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Matrix protein p15]: Virion {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Capsid protein p30]: Virion {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Nucleocapsid protein p10]: Virion {ECO:0000305}.
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       RNA-binding phosphoprotein p12 contains one L domain: a PPXY motif
CC       which potentially interacts with the WW domain 3 of NEDD4 E3 ubiquitin
CC       ligase. PPXY motif is essential for virus egress. Matrix protein p15
CC       contains one L domain: a PTAP/PSAP motif, which potentially interacts
CC       with the UEV domain of TSG101. The junction between the matrix protein
CC       p15 and RNA-binding phosphoprotein p12 also contains one L domain: a
CC       LYPX(n)L motif which potentially interacts with PDCD6IP. Both PSAP and
CC       LYPX(n)L domains might play little to no role in budding and possibly
CC       drive residual virus release. contains. {ECO:0000250|UniProtKB:P03332}.
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.
CC       {ECO:0000250|UniProtKB:P03355}.
CC   -!- PTM: [Capsid protein p30]: Sumoylated; which is required for virus
CC       replication. {ECO:0000250|UniProtKB:P03355}.
CC   -!- PTM: [RNA-binding phosphoprotein p12]: Phosphorylated on serine
CC       residues. {ECO:0000250|UniProtKB:P03355}.
CC   -!- MISCELLANEOUS: [Gag-Pol polyprotein]: This protein is translated as a
CC       gag-pol fusion protein by episodic readthrough of the gag protein
CC       termination codon. Readthrough of the terminator codon TAG occurs
CC       between the codons for 536-Asp and 538-Gly.
CC       {ECO:0000250|UniProtKB:P03355}.
CC   -!- MISCELLANEOUS: [Nucleocapsid protein p10]: Nucleocapsid protein p10
CC       released from Pol polyprotein (NC-pol) is a few amino acids shorter
CC       than the nucleocapsid protein p10 released from Gag polyprotein (NC-
CC       gag). {ECO:0000250}.
CC   -!- MISCELLANEOUS: [Reverse transcriptase/ribonuclease H p80]: The reverse
CC       transcriptase is an error-prone enzyme that lacks a proof-reading
CC       function. High mutations rate is a direct consequence of this
CC       characteristic. RT also displays frequent template swiching leading to
CC       high recombination rate. Recombination mostly occurs between homologous
CC       regions of the two copackaged RNA genomes. If these two RNA molecules
CC       derive from different viral strains, reverse transcription will give
CC       rise to highly recombinated proviral DNAs. {ECO:0000255|PROSITE-
CC       ProRule:PRU00405}.
CC   -!- CAUTION: Originally thought to be characterized from prostate tumors,
CC       the described gammaretrovirus XMRV is in fact laboratory-derived and
CC       there is no association of XMRV with prostate cancer.
CC       {ECO:0000305|PubMed:16609730, ECO:0000305|PubMed:23028303}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; DQ241301; ABB83225.1; -; Genomic_RNA.
DR   PDB; 3V1O; X-ray; 1.88 A; A=1154-1328.
DR   PDB; 3V1Q; X-ray; 2.00 A; A=1155-1328.
DR   PDB; 3V1R; X-ray; 2.80 A; A=1154-1328.
DR   PDBsum; 3V1O; -.
DR   PDBsum; 3V1Q; -.
DR   PDBsum; 3V1R; -.
DR   SMR; Q2F7J3; -.
DR   Proteomes; UP000008601; Genome.
DR   GO; GO:0020002; C:host cell plasma membrane; 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: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:0039660; F:structural constituent of virion; IEA:UniProtKB-KW.
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: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:0019068; P:virion assembly; IEA:InterPro.
DR   CDD; cd09273; RNase_HI_RT_Bel; 1.
DR   CDD; cd06095; RP_RTVL_H_like; 1.
DR   CDD; cd03715; RT_ZFREV_like; 1.
DR   Gene3D; 1.10.340.70; -; 1.
DR   Gene3D; 2.30.30.850; -; 1.
DR   Gene3D; 3.10.20.370; -; 1.
DR   Gene3D; 3.30.70.270; -; 2.
DR   Gene3D; 2.40.70.10; Acid Proteases; 1.
DR   Gene3D; 1.10.150.180; Gamma-retroviral matrix domain; 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; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 2.
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; IPR000840; G_retro_matrix.
DR   InterPro; IPR036946; G_retro_matrix_sf.
DR   InterPro; IPR039464; Gag-pol_Znf-H3C2.
DR   InterPro; IPR002079; Gag_p12.
DR   InterPro; IPR003036; Gag_P30.
DR   InterPro; IPR001584; Integrase_cat-core.
DR   InterPro; IPR040643; MLVIN_C.
DR   InterPro; IPR001995; Peptidase_A2_cat.
DR   InterPro; IPR021109; Peptidase_aspartic_dom_sf.
DR   InterPro; IPR018061; Retropepsins.
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; IPR041577; RT_RNaseH_2.
DR   InterPro; IPR001878; Znf_CCHC.
DR   InterPro; IPR036875; Znf_CCHC_sf.
DR   PANTHER; PTHR33166:SF1; CORE SHELL PROTEIN GAG P30 DOMAIN-CONTAINING PROTEIN; 1.
DR   PANTHER; PTHR33166; GAG_P30 DOMAIN-CONTAINING PROTEIN; 1.
DR   Pfam; PF01140; Gag_MA; 1.
DR   Pfam; PF01141; Gag_p12; 1.
DR   Pfam; PF02093; Gag_p30; 1.
DR   Pfam; PF18697; MLVIN_C; 1.
DR   Pfam; PF00075; RNase_H; 1.
DR   Pfam; PF17919; RT_RNaseH_2; 1.
DR   Pfam; PF00665; rve; 1.
DR   Pfam; PF00077; RVP; 1.
DR   Pfam; PF00078; RVT_1; 1.
DR   Pfam; PF00098; zf-CCHC; 1.
DR   Pfam; PF16721; zf-H3C2; 1.
DR   SMART; SM00343; ZnF_C2HC; 1.
DR   SUPFAM; SSF50630; Acid proteases; 1.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   SUPFAM; SSF47836; Retroviral matrix proteins; 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; PS50879; RNASE_H_1; 1.
DR   PROSITE; PS50878; RT_POL; 1.
DR   PROSITE; PS50158; ZF_CCHC; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Aspartyl protease; Capsid protein; Coiled coil;
KW   DNA integration; DNA recombination; DNA-binding;
KW   DNA-directed DNA polymerase; Endonuclease; Host cell membrane;
KW   Host membrane; Hydrolase; Lipoprotein; Magnesium; Manganese; Membrane;
KW   Metal-binding; Multifunctional enzyme; Myristate; Nuclease;
KW   Nucleotidyltransferase; Phosphoprotein; Protease;
KW   RNA suppression of termination; RNA-binding; RNA-directed DNA polymerase;
KW   Transferase; Ubl conjugation; Viral genome integration;
KW   Viral matrix protein; Viral nucleoprotein; Virion;
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..1733
FT                   /note="Gag-Pol polyprotein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390852"
FT   CHAIN           2..129
FT                   /note="Matrix protein p15"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390853"
FT   CHAIN           130..213
FT                   /note="RNA-binding phosphoprotein p12"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390854"
FT   CHAIN           214..476
FT                   /note="Capsid protein p30"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390855"
FT   CHAIN           477..532
FT                   /note="Nucleocapsid protein p10"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390856"
FT   CHAIN           533..657
FT                   /note="Protease p14"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390857"
FT   CHAIN           658..1328
FT                   /note="Reverse transcriptase/ribonuclease H p80"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390858"
FT   CHAIN           1329..1733
FT                   /note="Integrase p46"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000390859"
FT   DOMAIN          559..629
FT                   /note="Peptidase A2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00275"
FT   DOMAIN          739..930
FT                   /note="Reverse transcriptase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT   DOMAIN          1172..1318
FT                   /note="RNase H type-1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT   DOMAIN          1442..1600
FT                   /note="Integrase catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT   ZN_FING         500..517
FT                   /note="CCHC-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT   REGION          99..218
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          474..495
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          511..550
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          436..476
FT                   /evidence="ECO:0000255"
FT   MOTIF           109..112
FT                   /note="PTAP/PSAP motif"
FT   MOTIF           128..132
FT                   /note="LYPX(n)L motif"
FT   MOTIF           161..164
FT                   /note="PPXY motif"
FT   COMPBIAS        99..123
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        164..190
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        564
FT                   /note="Protease; shared with dimeric partner"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00275"
FT   BINDING         721
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         771
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         773
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         787
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         807
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         851
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         853
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         881
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         882
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         941
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         955
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         958
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         966
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1054
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1055
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1063
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1082
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1113
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1181
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:PRU00408,
FT                   ECO:0000269|PubMed:22366278"
FT   BINDING         1181
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00408,
FT                   ECO:0000269|PubMed:22366278"
FT   BINDING         1184
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1186
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1187
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1214
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1216
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /ligand_note="DNA primer"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1219
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00408,
FT                   ECO:0000269|PubMed:22366278"
FT   BINDING         1240
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /ligand_note="catalytic; for RNase H activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00408,
FT                   ECO:0000269|PubMed:22366278"
FT   BINDING         1242
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1266
FT                   /ligand="RNA"
FT                   /ligand_id="ChEBI:CHEBI:33697"
FT                   /ligand_note="RNA template"
FT                   /evidence="ECO:0000250|UniProtKB:A1Z651"
FT   BINDING         1310
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:PRU00408,
FT                   ECO:0000269|PubMed:22366278"
FT   BINDING         1453
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="4"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         1512
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="4"
FT                   /ligand_note="catalytic; for integrase activity"
FT                   /evidence="ECO:0000250"
FT   SITE            129..130
FT                   /note="Cleavage; by viral protease p14"
FT                   /evidence="ECO:0000250"
FT   SITE            213..214
FT                   /note="Cleavage; by viral protease p14"
FT                   /evidence="ECO:0000250"
FT   SITE            476..477
FT                   /note="Cleavage; by viral protease p14"
FT                   /evidence="ECO:0000250"
FT   SITE            532..533
FT                   /note="Cleavage; by viral protease p14"
FT                   /evidence="ECO:0000250"
FT   SITE            657..658
FT                   /note="Cleavage; by viral protease p14"
FT                   /evidence="ECO:0000250"
FT   SITE            1328..1329
FT                   /note="Cleavage; by viral protease p14"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         190
FT                   /note="Phosphoserine; by host"
FT                   /evidence="ECO:0000250"
FT   LIPID           2
FT                   /note="N-myristoyl glycine; by host"
FT                   /evidence="ECO:0000250"
FT   STRAND          1167..1169
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1175..1186
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1188..1198
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1200..1209
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   HELIX           1215..1229
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   TURN            1230..1232
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1233..1240
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   HELIX           1242..1249
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   HELIX           1251..1257
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1261..1264
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1268..1270
FT                   /evidence="ECO:0007829|PDB:3V1Q"
FT   HELIX           1271..1280
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   STRAND          1283..1291
FT                   /evidence="ECO:0007829|PDB:3V1O"
FT   HELIX           1301..1322
FT                   /evidence="ECO:0007829|PDB:3V1O"
SQ   SEQUENCE   1733 AA;  193803 MW;  35B226FA584B5122 CRC64;
     MGQTVTTPLS LTLQHWGDVQ RIASNQSVDV KKRRWVTFCS AEWPTFNVGW PQDGTFNLGV
     ISQVKSRVFC PGPHGHPDQV PYIVTWEALA YDPPPWVKPF VSPKPPPLPT APVLPPGPSA
     QPPSRSALYP ALTLSIKSKP PKPQVLPDSG GPLIDLLTED PPPYGVQPSS SARENNEEEA
     ATTSEVSPPS PMVSRLRGRR DPPAADSTTS QAFPLRMGGD GQLQYWPFSS SDLYNWKNNN
     PSFSEDPGKL TALIESVLIT HQPTWDDCQQ LLGTLLTGEE KQRVLLEAGK AVRGNDGRPT
     QLPNEVNAAF PLERPDWDYT TTEGRNHLVL YRQLLLAGLQ NAGRSPTNLA KVKGITQGPN
     ESPSAFLERL KEAYRRYTPY DPEDPGQETN VSMSFIWQSA PDIGRKLERL EDLKSKTLGD
     LVREAEKIFN KRETPEEREE RIRREIEEKE ERRRAEDEQR ERERDRRRHR EMSKLLATVV
     IGQRQDRQGG ERRRPQLDKD QCAYCKEKGH WAKDCPKKPR GPRGPRPQTS LLTLGDXGGQ
     GQEPPPEPRI TLKVGGQPVT FLVDTGAQHS VLTQNPGPLS DKSAWVQGAT GGKRYRWTTD
     RKVHLATGKV THSFLHVPDC PYPLLGRDLL TKLKAQIHFE GSGAQVVGPM GQPLQVLTLN
     IENKYRLHET SKEPDVPLGS TWLSDFPQAW AETGGMGLAV RQAPLIIPLK ATSTPVSIKQ
     YPMSQEARLG IKPHIQRLLD QGILVPCQSP WNTPLLPVKK PGTNDYRPVQ DLREVNKRVE
     DIHPTVPNPY NLLSGLPPSH QWYTVLDLKD AFFCLRLHPT SQPLFAFEWR DPEMGISGQL
     TWTRLPQGFK NSPTLFDEAL HRDLADFRIQ HPDLILLQYV DDLLLAATSE QDCQRGTRAL
     LQTLGNLGYR ASAKKAQICQ KQVKYLGYLL KEGQRWLTEA RKETVMGQPT PKTPRQLREF
     LGTAGFCRLW IPGFAEMAAP LYPLTKTGTL FNWGPDQQKA YQEIKQALLT APALGLPDLT
     KPFELFVDEK QGYAKGVLTQ KLGPWRRPVA YLSKKLDPVA AGWPPCLRMV AAIAVLTKDA
     GKLTMGQPLV ILAPHAVEAL VKQPPDRWLS NARMTHYQAM LLDTDRVQFG PVVALNPATL
     LPLPEKEAPH DCLEILAETH GTRPDLTDQP IPDADYTWYT DGSSFLQEGQ RRAGAAVTTE
     TEVIWARALP AGTSAQRAEL IALTQALKMA EGKKLNVYTD SRYAFATAHV HGEIYRRRGL
     LTSEGREIKN KNEILALLKA LFLPKRLSII HCPGHQKGNS AEARGNRMAD QAAREAAMKA
     VLETSTLLIE DSTPYTPPHF HYTETDLKRL RELGATYNQT KGYWVLQGKP VMPDQSVFEL
     LDSLHRLTHP SPQKMKALLD REESPYYMLN RDRTIQYVTE TCTACAQVNA SKAKIGAGVR
     VRGHRPGTHW EVDFTEVKPG LYGYKYLLVF VDTFSGWVEA FPTKRETAKV VTKKLLEDIF
     PRFGMPQVLG SDNGPAFASQ VSQSVADLLG IDWKLHCAYR PQSSGQVERM NRTIKETLTK
     LTLASGTRDW VLLLPLALYR ARNTPGPHGL TPYEILYGAP PPLVNFHDPE MSKLTNSPSL
     QAHLQALQAV QQEVWKPLAA AYQDQLDQPV IPHPFRVGDA VWVRRHQTKN LEPRWKGPYT
     VLLTTPTALK VDGISAWIHA AHVKAATTPP AGTAWKVQRS QNPLKIRLTR GAP
//