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POL_HV1J3
ID   POL_HV1J3               Reviewed;         532 AA.
AC   P12498;
DT   01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 4.
DT   03-AUG-2022, entry version 166.
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=3.4.23.16;
DE     AltName: Full=PR;
DE     AltName: Full=Retropepsin;
DE   Flags: Fragment;
GN   Name=gag-pol;
OS   Human immunodeficiency virus type 1 group M subtype B (isolate JH32)
OS   (HIV-1).
OC   Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC   Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX   NCBI_TaxID=11694;
OH   NCBI_TaxID=9606; Homo sapiens (Human).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=2669897; DOI=10.1089/aid.1989.5.411;
RA   Komiyama N., Hattori N., Inoue J., Sakuma S., Kurimura T., Yoshida M.;
RT   "Nucleotide sequences of gag and env genes of a Japanese isolate of HIV-1
RT   and their expression in bacteria.";
RL   AIDS Res. Hum. Retroviruses 5:411-419(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).
RN   [6]
RP   REVIEW.
RX   PubMed=12873766; DOI=10.1016/s0005-2736(03)00163-9;
RA   Scarlata S., Carter C.;
RT   "Role of HIV-1 Gag domains in viral assembly.";
RL   Biochim. Biophys. Acta 1614:62-72(2003).
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. Also mediates cleavage of
CC       host YTHDF3. Mediates cleavage of host CARD8, thereby activating the
CC       CARD8 inflammasome, leading to the clearance of latent HIV-1 in patient
CC       CD4(+) T-cells after viral reactivation; in contrast, HIV-1 can evade
CC       CARD8-sensing when its protease remains inactive in infected cells
CC       prior to viral budding (By similarity). {ECO:0000250|UniProtKB:P04585,
CC       ECO:0000255|PROSITE-ProRule:PRU00275}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Specific for a P1 residue that is hydrophobic, and P1'
CC         variable, but often Pro.; EC=3.4.23.16;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00275};
CC   -!- ACTIVITY REGULATION: [Protease]: The viral protease is inhibited by
CC       many synthetic protease inhibitors (PIs), such as amprenavir,
CC       atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and
CC       saquinavir. Use of protease inhibitors in tritherapy regimens permit
CC       more ambitious therapeutic strategies. {ECO:0000250}.
CC   -!- SUBUNIT: [Matrix protein p17]: Homotrimer; further assembles as
CC       hexamers of trimers (By similarity). Interacts with gp41 (via C-
CC       terminus) (By similarity). Interacts with host CALM1; this interaction
CC       induces a conformational change in the Matrix protein, triggering
CC       exposure of the myristate group (By similarity). Interacts with host
CC       AP3D1; this interaction allows the polyprotein trafficking to
CC       multivesicular bodies during virus assembly (By similarity). Part of
CC       the pre-integration complex (PIC) which is composed of viral genome,
CC       matrix protein, Vpr and integrase (By similarity).
CC       {ECO:0000250|UniProtKB:P04585, ECO:0000250|UniProtKB:P12497}.
CC   -!- SUBUNIT: [Capsid protein p24]: Homodimer; the homodimer further
CC       multimerizes as homohexamers or homopentamers. Interacts with human
CC       PPIA/CYPA (By similarity); This interaction stabilizes the capsid.
CC       Interacts with human NUP153 (By similarity). Interacts with host PDZD8;
CC       this interaction stabilizes the capsid (By similarity). Interacts with
CC       monkey TRIM5; this interaction destabilizes the capsid (By similarity).
CC       {ECO:0000250|UniProtKB:P04585, ECO:0000250|UniProtKB:P12497}.
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   -!- 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   -!- 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=P12498-1; Sequence=Displayed;
CC       Name=Gag polyprotein;
CC         IsoId=P12494-1; Sequence=External;
CC   -!- PTM: Specific enzymatic cleavages by the viral protease yield mature
CC       proteins. The protease is released by autocatalytic cleavage. The
CC       polyprotein is cleaved during and after budding, this process is termed
CC       maturation. Proteolytic cleavage of p66 RT removes the RNase H domain
CC       to yield the p51 RT subunit. Nucleocapsid protein p7 might be further
CC       cleaved after virus entry (By similarity). {ECO:0000250}.
CC   -!- PTM: [Matrix protein p17]: Tyrosine phosphorylated presumably in the
CC       virion by a host kinase. Phosphorylation is apparently not a major
CC       regulator of membrane association. {ECO:0000250|UniProtKB:P04585}.
CC   -!- PTM: [Capsid protein p24]: Phosphorylated possibly by host MAPK1; this
CC       phosphorylation is necessary for Pin1-mediated virion uncoating.
CC       {ECO:0000250|UniProtKB:P12493}.
CC   -!- PTM: [Nucleocapsid protein p7]: Methylated by host PRMT6, impairing its
CC       function by reducing RNA annealing and the initiation of reverse
CC       transcription. {ECO:0000250|UniProtKB:P03347}.
CC   -!- MISCELLANEOUS: HIV-1 lineages are divided in three main groups, M (for
CC       Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast
CC       majority of strains found worldwide belong to the group M. Group O
CC       seems to be endemic to and largely confined to Cameroon and neighboring
CC       countries in West Central Africa, where these viruses represent a small
CC       minority of HIV-1 strains. The group N is represented by a limited
CC       number of isolates from Cameroonian persons. The group M is further
CC       subdivided in 9 clades or subtypes (A to D, F to H, J and K).
CC   -!- MISCELLANEOUS: Resistance to inhibitors associated with mutations are
CC       observed both in viral protease and in reverse transcriptase. Most of
CC       the time, single mutations confer only a modest reduction in drug
CC       susceptibility. Combination of several mutations is usually required to
CC       develop a high-level drug resistance. These mutations are predominantly
CC       found in clade B viruses and not in other genotypes. They are listed in
CC       the clade B representative isolate HXB2 (AC P04585).
CC   -!- MISCELLANEOUS: [Isoform Gag-Pol polyprotein]: Produced by -1 ribosomal
CC       frameshifting.
CC   -!- WEB RESOURCE: Name=HIV drug resistance mutations;
CC       URL="https://www.iasusa.org/content/hiv-drug-resistance-mutations";
CC   -!- WEB RESOURCE: Name=hivdb; Note=HIV drug resistance database;
CC       URL="https://hivdb.stanford.edu";
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DR   EMBL; M21137; AAB03523.1; ALT_SEQ; Genomic_RNA.
DR   SMR; P12498; -.
DR   MEROPS; A02.001; -.
DR   PRO; PR:P12498; -.
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:0008289; F:lipid binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
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   Gene3D; 1.10.1200.30; -; 1.
DR   Gene3D; 1.10.150.90; -; 1.
DR   Gene3D; 1.10.375.10; -; 1.
DR   Gene3D; 2.40.70.10; -; 1.
DR   InterPro; IPR001969; Aspartic_peptidase_AS.
DR   InterPro; IPR045345; Gag_p24_C.
DR   InterPro; IPR000721; Gag_p24_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; IPR018061; Retropepsins.
DR   InterPro; IPR008916; Retrov_capsid_C.
DR   InterPro; IPR008919; Retrov_capsid_N.
DR   InterPro; IPR010999; Retrovr_matrix.
DR   InterPro; IPR001878; Znf_CCHC.
DR   InterPro; IPR036875; Znf_CCHC_sf.
DR   Pfam; PF00540; Gag_p17; 1.
DR   Pfam; PF00607; Gag_p24; 1.
DR   Pfam; PF19317; Gag_p24_C; 1.
DR   Pfam; PF00077; RVP; 1.
DR   Pfam; PF00098; zf-CCHC; 2.
DR   PRINTS; PR00234; HIV1MATRIX.
DR   SMART; SM00343; ZnF_C2HC; 2.
DR   SUPFAM; SSF47836; SSF47836; 1.
DR   SUPFAM; SSF47943; SSF47943; 1.
DR   SUPFAM; SSF50630; SSF50630; 1.
DR   SUPFAM; SSF57756; SSF57756; 1.
DR   PROSITE; PS50175; ASP_PROT_RETROV; 1.
DR   PROSITE; PS00141; ASP_PROTEASE; 1.
DR   PROSITE; PS50158; ZF_CCHC; 2.
PE   3: Inferred from homology;
KW   AIDS; Aspartyl protease; Capsid protein;
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; Membrane; Metal-binding; Myristate;
KW   Phosphoprotein; Protease; Repeat; Ribosomal frameshifting; RNA-binding;
KW   Viral nucleoprotein; Viral release from host cell; Virion;
KW   Virion maturation; Zinc; Zinc-finger.
FT   INIT_MET        1
FT                   /note="Removed; by host"
FT                   /evidence="ECO:0000250"
FT   CHAIN           2..>532
FT                   /note="Gag-Pol polyprotein"
FT                   /id="PRO_0000261268"
FT   CHAIN           2..132
FT                   /note="Matrix protein p17"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042362"
FT   CHAIN           133..363
FT                   /note="Capsid protein p24"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042363"
FT   PEPTIDE         364..377
FT                   /note="Spacer peptide 1"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042364"
FT   CHAIN           378..432
FT                   /note="Nucleocapsid protein p7"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000042365"
FT   PEPTIDE         433..440
FT                   /note="Transframe peptide"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000246717"
FT   CHAIN           441..488
FT                   /note="p6-pol"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000042366"
FT   CHAIN           489..>532
FT                   /note="Protease"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000038656"
FT   DOMAIN          508..>532
FT                   /note="Peptidase A2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00275"
FT   ZN_FING         390..407
FT                   /note="CCHC-type 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT   ZN_FING         411..428
FT                   /note="CCHC-type 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT   REGION          7..31
FT                   /note="Interaction with Gp41"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          8..43
FT                   /note="Interaction with host CALM1"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   REGION          12..19
FT                   /note="Interaction with host AP3D1"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          14..33
FT                   /note="Interaction with membrane phosphatidylinositol 4,5-
FT                   bisphosphate and RNA"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          73..77
FT                   /note="Interaction with membrane phosphatidylinositol 4,5-
FT                   bisphosphate"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          106..127
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          189..227
FT                   /note="Interaction with human PPIA/CYPA and NUP153"
FT                   /evidence="ECO:0000250|UniProtKB:P12497"
FT   REGION          277..363
FT                   /note="Dimerization/Multimerization of capsid protein p24"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
FT   REGION          447..481
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          489..493
FT                   /note="Dimerization of protease"
FT                   /evidence="ECO:0000250|UniProtKB:P04585"
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   COMPBIAS        447..464
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        513
FT                   /note="For protease activity; shared with dimeric partner"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10094"
FT   SITE            132..133
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            221..222
FT                   /note="Cis/trans isomerization of proline peptide bond; by
FT                   human PPIA/CYPA"
FT                   /evidence="ECO:0000250"
FT   SITE            363..364
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            377..378
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            432..433
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000255"
FT   SITE            440..441
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   SITE            488..489
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         132
FT                   /note="Phosphotyrosine; by host"
FT                   /evidence="ECO:0000250"
FT   LIPID           2
FT                   /note="N-myristoyl glycine; by host"
FT                   /evidence="ECO:0000250"
FT   NON_TER         532
SQ   SEQUENCE   532 AA;  59412 MW;  C47419992DFC78D6 CRC64;
     MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPSL LETSEGCRQI
     LGQLQPSLQT GSEELKSLFN TVATLYCVHQ RIEVKDTKEA LEKIEEEQNK SKKKAQQAAA
     DTGNSSKVSQ NYPIVQNIQG QMVHQAISPR TLNAWVKVVE EKAFSPEVIP MFSALSEGAT
     PQDLNTMLNT VGGHQAAMQM LKETINEEAA EWDRLHPAQA GPIAPGQMRE PRGSDIAGTT
     STLQEQIGWM TSNPPIPVGE IYKRWIILGL NKIVRMYSPS SILDIRQGPK EPFRDYVDRF
     YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC QGVGGPGHKA
     RVLAEAMSQV TNSTTIMMQR GNFRNQRKII KCFNCGKEGH LARNCRAPRK KGCWKCGKEG
     HQMKDCNERQ ANFLREDLAF LQGKAREFSS EQTRANSPSR GELQVWGRDN NPLSEAGAER
     QGTVSFSFPQ ITLWQRPLVT LKIGGQLKEA LLDTGADDTV LEEMNSPGRW KP
 
 
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