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Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]

 POL_HV1ET               Reviewed;        1439 AA.
Q75002;
25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
07-JUN-2017, entry version 142.
RecName: Full=Gag-Pol polyprotein;
AltName: Full=Pr160Gag-Pol;
Contains:
RecName: Full=Matrix protein p17;
Short=MA;
Contains:
RecName: Full=Capsid protein p24;
Short=CA;
Contains:
RecName: Full=Spacer peptide 1 {ECO:0000250|UniProtKB:P12497};
Short=SP1;
AltName: Full=p2;
Contains:
RecName: Full=Nucleocapsid protein p7;
Short=NC;
Contains:
RecName: Full=Transframe peptide;
Short=TF;
Contains:
RecName: Full=p6-pol;
Short=p6*;
Contains:
RecName: Full=Protease;
EC=3.4.23.16;
AltName: Full=PR;
AltName: Full=Retropepsin;
Contains:
RecName: Full=Reverse transcriptase/ribonuclease H;
EC=2.7.7.49;
EC=2.7.7.7;
EC=3.1.26.13;
AltName: Full=Exoribonuclease H;
EC=3.1.13.2;
AltName: Full=p66 RT;
Contains:
RecName: Full=p51 RT;
Contains:
RecName: Full=p15;
Contains:
RecName: Full=Integrase;
Short=IN;
EC=2.7.7.- {ECO:0000250|UniProtKB:P04585};
EC=3.1.-.- {ECO:0000250|UniProtKB:P04585};
Name=gag-pol;
Human immunodeficiency virus type 1 group M subtype C (isolate
ETH2220) (HIV-1).
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae;
Lentivirus; Primate lentivirus group.
NCBI_TaxID=388796;
NCBI_TaxID=9606; Homo sapiens (Human).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=8891112; DOI=10.1089/aid.1996.12.1329;
Salminen M.O., Johansson B., Sonnerborg A., Ayehunie S., Gotte D.,
Leinikki P., Burke D.S., McCutchan F.E.;
"Full-length sequence of an ethiopian human immunodeficiency virus
type 1 (HIV-1) isolate of genetic subtype C.";
AIDS Res. Hum. Retroviruses 12:1329-1339(1996).
-!- FUNCTION: Gag-Pol polyprotein: Mediates, with Gag polyrotein, the
essential events in virion assembly, including binding the plasma
membrane, making the protein-protein interactions necessary to
create spherical particles, recruiting the viral Env proteins, and
packaging the genomic RNA via direct interactions with the RNA
packaging sequence (Psi). Gag-Pol polyprotein may regulate its own
translation, by the binding genomic RNA in the 5'-UTR. At low
concentration, the polyprotein would promote translation, whereas
at high concentration, the polyprotein would encapsidate genomic
RNA and then shutt off translation. {ECO:0000250}.
-!- FUNCTION: Matrix protein p17: Targets the polyprotein to the
plasma membrane via a multipartite membrane-binding signal, that
includes its myristoylated N-terminus. Matrix protein is part of
the pre-integration complex. Implicated in the release from host
cell mediated by Vpu. Binds to RNA.
{ECO:0000250|UniProtKB:P12497}.
-!- FUNCTION: Capsid protein p24: Forms the conical core that
encapsulates the genomic RNA-nucleocapsid complex in the virion.
Most core are conical, with only 7% tubular. The core is
constituted by capsid protein hexamer subunits. The core is
disassembled soon after virion entry (By similarity). Host
restriction factors such as TRIM5-alpha or TRIMCyp bind retroviral
capsids and cause premature capsid disassembly, leading to blocks
in reverse transcription. Capsid restriction by TRIM5 is one of
the factors which restricts HIV-1 to the human species. Host PIN1
apparently facilitates the virion uncoating. On the other hand,
interactions with PDZD8 or CYPA stabilize the capsid.
{ECO:0000250|UniProtKB:P04585, ECO:0000250|UniProtKB:P12497}.
-!- FUNCTION: Nucleocapsid protein p7: Encapsulates and protects viral
dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its
zinc fingers. Acts as a nucleic acid chaperone which is involved
in rearangement of nucleic acid secondary structure during gRNA
retrotranscription. Also facilitates template switch leading to
recombination. As part of the polyprotein, participates in gRNA
dimerization, packaging, tRNA incorporation and virion assembly.
{ECO:0000250|UniProtKB:P04585}.
-!- FUNCTION: Protease: Aspartyl protease that mediates proteolytic
cleavages of Gag and Gag-Pol polyproteins during or shortly after
the release of the virion from the plasma membrane. Cleavages take
place as an ordered, step-wise cascade to yield mature proteins.
This process is called maturation. Displays maximal activity
during the budding process just prior to particle release from the
cell. Also cleaves Nef and Vif, probably concomitantly with viral
structural proteins on maturation of virus particles. Hydrolyzes
host EIF4GI and PABP1 in order to shut off the capped cellular
mRNA translation. The resulting inhibition of cellular protein
synthesis serves to ensure maximal viral gene expression and to
evade host immune response (By similarity).
{ECO:0000250|UniProtKB:P04585, ECO:0000255|PROSITE-
ProRule:PRU00275}.
-!- FUNCTION: Reverse transcriptase/ribonuclease H: Multifunctional
enzyme that converts the viral RNA genome into dsDNA in the
cytoplasm, shortly after virus entry into the cell. This enzyme
displays a DNA polymerase activity that can copy either DNA or RNA
templates, and a ribonuclease H (RNase H) activity that cleaves
the RNA strand of RNA-DNA heteroduplexes in a partially processive
3' to 5' endonucleasic mode. Conversion of viral genomic RNA into
dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-
binding site (PBS) situated at the 5'-end of the viral RNA. RT
uses the 3' end of the tRNA primer to perform a short round of
RNA-dependent minus-strand DNA synthesis. The reading proceeds
through the U5 region and ends after the repeated (R) region which
is present at both ends of viral RNA. The portion of the RNA-DNA
heteroduplex is digested by the RNase H, resulting in a ssDNA
product attached to the tRNA primer. This ssDNA/tRNA hybridizes
with the identical R region situated at the 3' end of viral RNA.
This template exchange, known as minus-strand DNA strong stop
transfer, can be either intra- or intermolecular. RT uses the 3'
end of this newly synthesized short ssDNA to perform the RNA-
dependent minus-strand DNA synthesis of the whole template. RNase
H digests the RNA template except for two polypurine tracts (PPTs)
situated at the 5'-end and near the center of the genome. It is
not clear if both polymerase and RNase H activities are
simultaneous. RNase H probably can proceed both in a polymerase-
dependent (RNA cut into small fragments by the same RT performing
DNA synthesis) and a polymerase-independent mode (cleavage of
remaining RNA fragments by free RTs). Secondly, RT performs DNA-
directed plus-strand DNA synthesis using the PPTs that have not
been removed by RNase H as primers. PPTs and tRNA primers are then
removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to
form a circular dsDNA intermediate. Strand displacement synthesis
by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA
copy of the viral genome that includes long terminal repeats
(LTRs) at both ends. {ECO:0000250|UniProtKB:P04585}.
-!- FUNCTION: Integrase: Catalyzes viral DNA integration into the host
chromosome, by performing a series of DNA cutting and joining
reactions. This enzyme activity takes place after virion entry
into a cell and reverse transcription of the RNA genome in dsDNA.
The first step in the integration process is 3' processing. This
step requires a complex comprising the viral genome, matrix
protein, Vpr and integrase. This complex is called the pre-
integration complex (PIC). The integrase protein removes 2
nucleotides from each 3' end of the viral DNA, leaving recessed CA
OH's at the 3' ends. In the second step, the PIC enters cell
nucleus. This process is mediated through integrase and Vpr
proteins, and allows the virus to infect a non dividing cell. This
ability to enter the nucleus is specific of lentiviruses, other
retroviruses cannot and rely on cell division to access cell
chromosomes. In the third step, termed strand transfer, the
integrase protein joins the previously processed 3' ends to the 5'
ends of strands of target cellular DNA at the site of integration.
The 5'-ends are produced by integrase-catalyzed staggered cuts, 5
bp apart. A Y-shaped, gapped, recombination intermediate results,
with the 5'-ends of the viral DNA strands and the 3' ends of
target DNA strands remaining unjoined, flanking a gap of 5 bp. The
last step is viral DNA integration into host chromosome. This
involves host DNA repair synthesis in which the 5 bp gaps between
the unjoined strands are filled in and then ligated. Since this
process occurs at both cuts flanking the HIV genome, a 5 bp
duplication of host DNA is produced at the ends of HIV-1
integration. Alternatively, Integrase may catalyze the excision of
viral DNA just after strand transfer, this is termed
disintegration. {ECO:0000250|UniProtKB:P04585}.
-!- CATALYTIC ACTIVITY: Specific for a P1 residue that is hydrophobic,
and P1' variable, but often Pro. {ECO:0000255|PROSITE-
ProRule:PRU00275}.
-!- CATALYTIC ACTIVITY: Endohydrolysis of RNA in RNA/DNA hybrids.
Three different cleavage modes: 1. sequence-specific internal
cleavage of RNA. Human immunodeficiency virus type 1 and Moloney
murine leukemia virus enzymes prefer to cleave the RNA strand one
nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed
cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end
directed cleavage 15-20 nucleotides away from the primer terminus.
{ECO:0000250}.
-!- CATALYTIC ACTIVITY: 3'-end directed exonucleolytic cleavage of
viral RNA-DNA hybrid. {ECO:0000250}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00405}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 2 magnesium ions for reverse transcriptase polymerase
activity. {ECO:0000250};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 2 magnesium ions for ribonuclease H (RNase H) activity.
Substrate-binding is a precondition for magnesium binding.
{ECO:0000250};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Magnesium ions are required for integrase activity. Binds at
least 1, maybe 2 magnesium ions. {ECO:0000250};
-!- ENZYME REGULATION: Protease: The viral protease is inhibited by
many synthetic protease inhibitors (PIs), such as amprenavir,
atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and
saquinavir. Use of protease inhibitors in tritherapy regimens
permit more ambitious therapeutic strategies. Reverse
transcriptase/ribonuclease H: RT can be inhibited either by
nucleoside RT inhibitors (NRTIs) or by non nucleoside RT
inhibitors (NNRTIs). NRTIs act as chain terminators, whereas
NNRTIs inhibit DNA polymerization by binding a small hydrophobic
pocket near the RT active site and inducing an allosteric change
in this region. Classical NRTIs are abacavir, adefovir (PMEA),
didanosine (ddI), lamivudine (3TC), stavudine (d4T), tenofovir
(PMPA), zalcitabine (ddC), and zidovudine (AZT). Classical NNRTIs
are atevirdine (BHAP U-87201E), delavirdine, efavirenz (DMP-266),
emivirine (I-EBU), and nevirapine (BI-RG-587). The tritherapies
used as a basic effective treatment of AIDS associate two NRTIs
and one NNRTI. {ECO:0000250}.
-!- SUBUNIT: Matrix protein p17: Homotrimer; further assembles as
hexamers of trimers (By similarity). Matrix protein p17: Interacts
with gp41 (via C-terminus) (By similarity). Matrix protein p17:
interacts with host CALM1; this interaction induces a
conformational change in the Matrix protein, triggering exposure
of the myristate group (By similarity). Matrix protein p17:
interacts with host AP3D1; this interaction allows the polyprotein
trafficking to multivesicular bodies during virus assembly (By
similarity). Matrix protein p17: Part of the pre-integration
complex (PIC) which is composed of viral genome, matrix protein,
Vpr and integrase (By similarity). Capsid protein p24: Homodimer;
the homodimer further multimerizes as homohexamers or
homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA
(By similarity); This interaction stabilizes the capsid. Capsid
protein p24: Interacts with human NUP153 (By similarity). Capsid
protein p24: Interacts with host PDZD8; this interaction
stabilizes the capsid (By similarity). Capsid protein p24:
Interacts with monkey TRIM5; this interaction destabilizes the
capsid (By similarity).Protease: Homodimer, whose active site
consists of two apposed aspartic acid residues. Reverse
transcriptase/ribonuclease H: Heterodimer of p66 RT and p51 RT (RT
p66/p51). Heterodimerization of RT is essential for DNA polymerase
activity. Despite the sequence identities, p66 RT and p51 RT have
distinct folding. Integrase: Homodimer; possibly can form
homotetramer. Integrase: Part of the pre-integration complex (PIC)
which is composed of viral genome, matrix protein, Vpr and
integrase. Integrase: Interacts with human SMARCB1/INI1 and human
PSIP1/LEDGF isoform 1. Integrase: Interacts with human KPNA3; this
interaction might play a role in nuclear import of the pre-
integration complex (By similarity). Integrase: Interacts with
human NUP153; this interaction might play a role in nuclear import
of the pre-integration complex (By similarity).
{ECO:0000250|UniProtKB:P04585, ECO:0000250|UniProtKB:P12497}.
-!- SUBCELLULAR LOCATION: Gag-Pol polyprotein: Host cell membrane;
Lipid-anchor. Host endosome, host multivesicular body. Note=These
locations are linked to virus assembly sites. The main location is
the cell membrane, but under some circumstances, late endosomal
compartments can serve as productive sites for virion assembly.
{ECO:0000250|UniProtKB:P12497}.
-!- SUBCELLULAR LOCATION: Matrix protein p17: Virion membrane; Lipid-
anchor {ECO:0000305}. Host nucleus {ECO:0000250}. Host cytoplasm
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Capsid protein p24: Virion {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Nucleocapsid protein p7: Virion
{ECO:0000305}.
-!- SUBCELLULAR LOCATION: Reverse transcriptase/ribonuclease H: Virion
{ECO:0000305}.
-!- SUBCELLULAR LOCATION: Integrase: Virion {ECO:0000305}. Host
nucleus {ECO:0000305}. Host cytoplasm {ECO:0000305}. Note=Nuclear
at initial phase, cytoplasmic at assembly. {ECO:0000305}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=2;
Comment=Translation results in the formation of the Gag
polyprotein most of the time. Ribosomal frameshifting at the
gag-pol genes boundary occurs at low frequency and produces the
Gag-Pol polyprotein. This strategy of translation probably
allows the virus to modulate the quantity of each viral protein.
Maintenance of a correct Gag to Gag-Pol ratio is essential for
RNA dimerization and viral infectivity.;
Name=Gag-Pol polyprotein;
IsoId=Q75002-1; Sequence=Displayed;
Note=Produced by -1 ribosomal frameshifting.;
Name=Gag polyprotein;
IsoId=Q75001-1; Sequence=External;
Note=Produced by conventional translation.;
-!- DOMAIN: Reverse transcriptase/ribonuclease H: RT is structured in
five subdomains: finger, palm, thumb, connection and RNase H.
Within the palm subdomain, the 'primer grip' region is thought to
be involved in the positioning of the primer terminus for
accommodating the incoming nucleotide. The RNase H domain
stabilizes the association of RT with primer-template.
{ECO:0000250}.
-!- DOMAIN: Reverse transcriptase/ribonuclease H: The tryptophan
repeat motif is involved in RT p66/p51 dimerization (By
similarity). {ECO:0000250}.
-!- DOMAIN: Integrase: The core domain contains the D-x(n)-D-x(35)-E
motif, named for the phylogenetically conserved glutamic acid and
aspartic acid residues and the invariant 35 amino acid spacing
between the second and third acidic residues. Each acidic residue
of the D,D(35)E motif is independently essential for the 3'-
processing and strand transfer activities of purified integrase
protein. {ECO:0000250}.
-!- PTM: Gag-Pol polyprotein: Specific enzymatic cleavages by the
viral protease yield mature proteins. The protease is released by
autocatalytic cleavage. The polyprotein is cleaved during and
after budding, this process is termed maturation. Proteolytic
cleavage of p66 RT removes the RNase H domain to yield the p51 RT
subunit. Nucleocapsid protein p7 might be further cleaved after
virus entry. {ECO:0000250|UniProtKB:P04585, ECO:0000255|PROSITE-
ProRule:PRU00405}.
-!- PTM: Matrix protein p17: Tyrosine phosphorylated presumably in the
virion by a host kinase. Phosphorylation is apparently not a major
regulator of membrane association. {ECO:0000250|UniProtKB:P04585}.
-!- PTM: Capsid protein p24: Phosphorylated possibly by host MAPK1;
this phosphorylation is necessary for Pin1-mediated virion
uncoating. {ECO:0000250|UniProtKB:P12493}.
-!- PTM: Nucleocapsid protein p7: Methylated by host PRMT6, impairing
its function by reducing RNA annealing and the initiation of
reverse transcription. {ECO:0000250|UniProtKB:P03347}.
-!- MISCELLANEOUS: Reverse transcriptase/ribonuclease H: Error-prone
enzyme that lacks a proof-reading function. High mutations rate is
a direct consequence of this characteristic. RT also displays
frequent template switching leading to high recombination rate.
Recombination mostly occurs between homologous regions of the two
copackaged RNA genomes. If these two RNA molecules derive from
different viral strains, reverse transcription will give rise to
highly recombinated proviral DNAs. {ECO:0000250}.
-!- MISCELLANEOUS: HIV-1 lineages are divided in three main groups, M
(for Major), O (for Outlier), and N (for New, or Non-M, Non-O).
The vast majority of strains found worldwide belong to the group
M. Group O seems to be endemic to and largely confined to Cameroon
and neighboring countries in West Central Africa, where these
viruses represent a small minority of HIV-1 strains. The group N
is represented by a limited number of isolates from Cameroonian
persons. The group M is further subdivided in 9 clades or subtypes
(A to D, F to H, J and K).
-!- MISCELLANEOUS: Resistance to inhibitors associated with mutations
are observed both in viral protease and in reverse transcriptase.
Most of the time, single mutations confer only a modest reduction
in drug susceptibility. Combination of several mutations is
usually required to develop a high-level drug resistance. These
mutations are predominantly found in clade B viruses and not in
other genotypes. They are listed in the clade B representative
isolate HXB2 (AC P04585).
-!- WEB RESOURCE: Name=HIV drug resistance mutations;
URL="https://www.iasusa.org/content/hiv-drug-resistance-mutations";
-!- WEB RESOURCE: Name=hivdb; Note=HIV drug resistance database;
URL="http://hivdb.stanford.edu";
-!- WEB RESOURCE: Name=BioAfrica: HIV bioinformatics in Africa;
URL="http://www.bioafrica.net/index.html";
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EMBL; U46016; AAB36501.1; ALT_SEQ; Genomic_DNA.
ProteinModelPortal; Q75002; -.
SMR; Q75002; -.
PRIDE; Q75002; -.
OrthoDB; VOG09000135; -.
PRO; PR:Q75002; -.
Proteomes; UP000007694; Genome.
GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
GO; GO:0020002; C:host cell plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0072494; C:host multivesicular body; IEA:UniProtKB-SubCell.
GO; GO:0019013; C:viral nucleocapsid; IEA:UniProtKB-KW.
GO; GO:0055036; C:virion membrane; IEA:UniProtKB-SubCell.
GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004533; F:exoribonuclease H activity; IEA:UniProtKB-EC.
GO; GO:0008289; F:lipid binding; IEA:UniProtKB-KW.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:InterPro.
GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
GO; GO:0039651; P:induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process; IEA:UniProtKB-KW.
GO; GO:0039657; P:suppression by virus of host gene expression; IEA:UniProtKB-KW.
GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
GO; GO:0075732; P:viral penetration into host nucleus; IEA:UniProtKB-KW.
GO; GO:0019076; P:viral release from host cell; IEA:UniProtKB-KW.
CDD; cd05482; HIV_retropepsin_like; 1.
Gene3D; 1.10.10.200; -; 1.
Gene3D; 1.10.1200.30; -; 1.
Gene3D; 1.10.375.10; -; 1.
Gene3D; 2.30.30.10; -; 1.
Gene3D; 2.40.70.10; -; 1.
Gene3D; 3.30.420.10; -; 2.
Gene3D; 4.10.60.10; -; 3.
InterPro; IPR001969; Aspartic_peptidase_AS.
InterPro; IPR000721; Gag_p24.
InterPro; IPR001037; Integrase_C_retrovir.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR017856; Integrase_Zn-bd_dom-like_N.
InterPro; IPR003308; Integrase_Zn-bd_dom_N.
InterPro; IPR000071; Lentvrl_matrix_N.
InterPro; IPR001995; Peptidase_A2_cat.
InterPro; IPR021109; Peptidase_aspartic_dom.
InterPro; IPR034170; Retropepsin-like_cat_dom.
InterPro; IPR018061; Retropepsins.
InterPro; IPR008916; Retrov_capsid_C.
InterPro; IPR008919; Retrov_capsid_N.
InterPro; IPR010999; Retrovr_matrix.
InterPro; IPR012337; RNaseH-like_dom.
InterPro; IPR002156; RNaseH_domain.
InterPro; IPR000477; RT_dom.
InterPro; IPR010659; RVT_connect.
InterPro; IPR010661; RVT_thumb.
InterPro; IPR001878; Znf_CCHC.
Pfam; PF00540; Gag_p17; 1.
Pfam; PF00607; Gag_p24; 1.
Pfam; PF00552; IN_DBD_C; 1.
Pfam; PF02022; Integrase_Zn; 1.
Pfam; PF00075; RNase_H; 1.
Pfam; PF00665; rve; 1.
Pfam; PF00077; RVP; 1.
Pfam; PF00078; RVT_1; 1.
Pfam; PF06815; RVT_connect; 1.
Pfam; PF06817; RVT_thumb; 1.
Pfam; PF00098; zf-CCHC; 2.
PRINTS; PR00234; HIV1MATRIX.
SMART; SM00343; ZnF_C2HC; 2.
SUPFAM; SSF46919; SSF46919; 1.
SUPFAM; SSF47353; SSF47353; 1.
SUPFAM; SSF47836; SSF47836; 1.
SUPFAM; SSF47943; SSF47943; 1.
SUPFAM; SSF50122; SSF50122; 1.
SUPFAM; SSF50630; SSF50630; 1.
SUPFAM; SSF53098; SSF53098; 2.
SUPFAM; SSF57756; SSF57756; 1.
PROSITE; PS50175; ASP_PROT_RETROV; 1.
PROSITE; PS00141; ASP_PROTEASE; 1.
PROSITE; PS50994; INTEGRASE; 1.
PROSITE; PS51027; INTEGRASE_DBD; 1.
PROSITE; PS50879; RNASE_H; 1.
PROSITE; PS50878; RT_POL; 1.
PROSITE; PS50158; ZF_CCHC; 2.
PROSITE; PS50876; ZF_INTEGRASE; 1.
3: Inferred from homology;
Activation of host caspases by virus; AIDS; Aspartyl protease;
Capsid protein; Complete proteome; DNA integration; DNA recombination;
DNA-binding; DNA-directed DNA polymerase; Endonuclease;
Eukaryotic host gene expression shutoff by virus;
Eukaryotic host translation shutoff by virus; Host cell membrane;
Host cytoplasm; Host endosome; Host gene expression shutoff by virus;
Host membrane; Host nucleus; Host-virus interaction; Hydrolase;
Lipid-binding; Lipoprotein; Magnesium; Membrane; Metal-binding;
Modulation of host cell apoptosis by virus; Multifunctional enzyme;
Myristate; Nuclease; Nucleotidyltransferase; Phosphoprotein; Protease;
Repeat; Ribosomal frameshifting; RNA-binding;
RNA-directed DNA polymerase; Transferase; Viral genome integration;
Viral nucleoprotein; Viral penetration into host nucleus; Virion;
Virion maturation; Virus entry into host cell;
Virus exit from host cell; Zinc; Zinc-finger.
INIT_MET 1 1 Removed; by host. {ECO:0000250}.
CHAIN 2 1439 Gag-Pol polyprotein.
/FTId=PRO_0000261267.
CHAIN 2 130 Matrix protein p17. {ECO:0000250}.
/FTId=PRO_0000246496.
CHAIN 131 361 Capsid protein p24. {ECO:0000250}.
/FTId=PRO_0000246497.
PEPTIDE 362 374 Spacer peptide 1. {ECO:0000250}.
/FTId=PRO_0000246498.
CHAIN 375 429 Nucleocapsid protein p7. {ECO:0000250}.
/FTId=PRO_0000246499.
PEPTIDE 430 437 Transframe peptide. {ECO:0000255}.
/FTId=PRO_0000246715.
CHAIN 438 492 p6-pol. {ECO:0000255}.
/FTId=PRO_0000246500.
CHAIN 493 591 Protease. {ECO:0000250}.
/FTId=PRO_0000246501.
CHAIN 592 1151 Reverse transcriptase/ribonuclease H.
{ECO:0000250}.
/FTId=PRO_0000246502.
CHAIN 592 1031 p51 RT. {ECO:0000250}.
/FTId=PRO_0000246503.
CHAIN 1032 1151 p15. {ECO:0000250}.
/FTId=PRO_0000246504.
CHAIN 1152 1439 Integrase. {ECO:0000250}.
/FTId=PRO_0000246505.
DOMAIN 512 581 Peptidase A2. {ECO:0000255|PROSITE-
ProRule:PRU00275}.
DOMAIN 635 825 Reverse transcriptase.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
DOMAIN 1025 1148 RNase H. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
DOMAIN 1205 1355 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
ZN_FING 387 404 CCHC-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 408 425 CCHC-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 1154 1195 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00450}.
DNA_BIND 1374 1421 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00506}.
REGION 7 31 Interaction with Gp41.
{ECO:0000250|UniProtKB:P12497}.
REGION 8 43 Interaction with host CALM1.
{ECO:0000250|UniProtKB:P04585}.
REGION 12 19 Interaction with host AP3D1.
{ECO:0000250|UniProtKB:P12497}.
REGION 14 33 Interaction with membrane
phosphatidylinositol 4,5-bisphosphate and
RNA. {ECO:0000250|UniProtKB:P12497}.
REGION 73 77 Interaction with membrane
phosphatidylinositol 4,5-bisphosphate.
{ECO:0000250|UniProtKB:P12497}.
REGION 187 225 Interaction with human PPIA/CYPA and
NUP153. {ECO:0000250|UniProtKB:P12497}.
REGION 275 361 Dimerization/Multimerization of capsid
protein p24.
{ECO:0000250|UniProtKB:P04585}.
REGION 493 497 Dimerization of protease.
{ECO:0000250|UniProtKB:P04585}.
REGION 541 547 Dimerization of protease.
{ECO:0000250|UniProtKB:P04585}.
REGION 580 592 Dimerization of protease.
{ECO:0000250|UniProtKB:P04585}.
REGION 818 826 RT 'primer grip'. {ECO:0000250}.
MOTIF 16 22 Nuclear export signal. {ECO:0000250}.
MOTIF 26 32 Nuclear localization signal.
{ECO:0000250}.
MOTIF 989 1005 Tryptophan repeat motif. {ECO:0000250}.
ACT_SITE 517 517 For protease activity; shared with
dimeric partner. {ECO:0000255|PROSITE-
ProRule:PRU10094}.
METAL 701 701 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 776 776 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 777 777 Magnesium; catalytic; for reverse
transcriptase activity. {ECO:0000250}.
METAL 1034 1034 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 1069 1069 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 1089 1089 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 1140 1140 Magnesium; catalytic; for RNase H
activity. {ECO:0000250}.
METAL 1215 1215 Magnesium; catalytic; for integrase
activity. {ECO:0000250}.
METAL 1267 1267 Magnesium; catalytic; for integrase
activity. {ECO:0000250}.
METAL 1303 1303 Magnesium; catalytic; for integrase
activity. {ECO:0000250|UniProtKB:P04585}.
SITE 130 131 Cleavage; by viral protease.
{ECO:0000250}.
SITE 219 220 Cis/trans isomerization of proline
peptide bond; by human PPIA/CYPA.
{ECO:0000250}.
SITE 361 362 Cleavage; by viral protease.
{ECO:0000250}.
SITE 374 375 Cleavage; by viral protease.
{ECO:0000250}.
SITE 429 430 Cleavage; by viral protease.
{ECO:0000255}.
SITE 437 438 Cleavage; by viral protease.
{ECO:0000250}.
SITE 492 493 Cleavage; by viral protease.
{ECO:0000250}.
SITE 591 592 Cleavage; by viral protease.
{ECO:0000250}.
SITE 992 992 Essential for RT p66/p51
heterodimerization. {ECO:0000250}.
SITE 1005 1005 Essential for RT p66/p51
heterodimerization. {ECO:0000250}.
SITE 1031 1032 Cleavage; by viral protease; partial.
{ECO:0000250}.
SITE 1151 1152 Cleavage; by viral protease.
{ECO:0000250}.
MOD_RES 130 130 Phosphotyrosine; by host. {ECO:0000250}.
LIPID 2 2 N-myristoyl glycine; by host.
{ECO:0000250}.
SEQUENCE 1439 AA; 162166 MW; 07AA53F13F9FD6E2 CRC64;
MGARASILRG EKLDAWEKIK LRPGGKKHYM LKHLVWANRE LEKFALNPDL LDTSAGCKQI
IKQLQPALQT GTEELKSLFN TVATLYCVHQ KIEIKDTKEA LDKIEEEQNE SQQKTQQAGA
ADRGKDSQNY PIVQNMQGQM VHQPISARTL NAWVKVVEEK AFSPEVIPMF TALSEGATPQ
DLNTMLNTVG GHQAAMQMLK DTINEEAAEW DRLHPVHAGP VAPGQMRDPR GSDIAGTTST
LQEQIAWMTG NPPVPVGDIY KRWIILGLNK IVRMYSPVSI LDIKQGPKEP FRDYVDRFFK
TLRAEQATQD VKNWMTDTLL VQNANPDCKT ILRALGPGAS LEEMMTACQG VGGPAHKARV
LAEAMSQVNN TTIMMQKSNF KGPKRAIKCF NCGKEGHLAR NCRAPRKKGC WKCGKEGHQM
KDCTERQANF FRETLAFQQG KAREFPSEQT RANSPTRESQ TRANSPTTRE LQVRGSNTFS
EAGAERQGSL NFPQITLWQR PLVTIKIGGQ LKEALLDTGA DDTVLEEINL PGKWKPKMIG
GIGGFIKVRQ YDQIIIEICG KKAIGTVLVG PTPVNIIGRN MLTQLGRTLN FPISPIETVP
VKLKPGMDGP KVKQWPLTEE KIKALTAICE EMEQEGKISR IGPENPYNTP VFAIKKKDST
KWRKLVDFRE LNKRTQDFWE VQLGIPHPAG LKKKKSVTVL DVGDAYFSVP LDEGFRKYTA
FTIPSTNNET PGIRYQYNVL PQGWKGSPPI FQSSMPQILE PFRAPNPEIV IYQYMDDLYV
GSDLEIGQHR APIEELREHL LKWGFTTPDK KHQKEPPFLW MGYELHPDKW TVQPIQLPEK
DSWTVNDIQK LVGKLNWASQ IYPGIKVRQL CKLLRGAKAL TDIVTLTEEA ELELAENREI
LKEPVHGVFY DPSKDLIAEI QKQGNDQWTF QFYQEPFKNL KTGKFAKRGT AHTNDVKQLT
AVVQKIALES IVIWGKTPKF RLPIQKETWE AWWTDYWQAT WIPEWEFVNT PPLVKLWYQL
EKEPIAGVET FYVDGAANRE TKIGKAGYVT DRGRQKIVSL TETTNQKTEL QAIQLALQDS
GSEVNIVTDS QYALGIILAQ PDKSESEIVN QIIEQLISKE RVYLSWVPAH KGIGGNEQVD
KLVSSGIRKV LFLDGIDKAQ EEHEKYHSNW RAMANEFNIP PVVPKEIVAC CDKCQLKGEA
IHGQVNCSPG IWQLDCTHLE GKIILVAVHV ASGYIEAEVI PAETGQETAY FLLKLAGRWP
VRVIHTDNGS NFTSNAVKAA CWWAGIQQEF GIPYNPQSQG VVESMNKELK KIIGQVREQA
EHLKTAVQMA VFIHNFKRRG GIGGYSAGER IIDIIASDIQ TKELQNQILK IQNFRVYYRD
SRDPIWKGPA KLLWKGEGAV VIQDNSDIKV VPRRKAKIIR DYGKQMAGAD CVAGRQDED


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