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UniProtKB - P0C6F2 (POL_HV1LW)

Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Human immunodeficiency virus type 1 group M subtype B (isolate LW123) (HIV-1)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Gag-Pol polyprotein: Mediates, with Gag polyprotein, 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 shut off translation.By similarity
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.By similarity
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.By similarity
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.By similarity
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).PROSITE-ProRule annotationBy similarity
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 tRNA3-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.By similarity
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.By similarity

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.By similarity
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).
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).

Catalytic activityi

Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.PROSITE-ProRule annotation
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.By similarity
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.By similarity
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarityNote: Binds 2 magnesium ions for reverse transcriptase polymerase activity.By similarity
  • Mg2+By similarityNote: Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.By similarity
  • Mg2+By similarityNote: Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.By similarity

Activity regulationi

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.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei221 – 222Cis/trans isomerization of proline peptide bond; by human PPIA/CYPABy similarity2
Active sitei513For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi697Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi772Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi773Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Sitei988Essential for RT p66/p51 heterodimerizationBy similarity1
Sitei1001Essential for RT p66/p51 heterodimerizationBy similarity1
Metal bindingi1030Magnesium; catalytic; for RNase H activity1 Publication1
Metal bindingi1065Magnesium; catalytic; for RNase H activity1 Publication1
Metal bindingi1085Magnesium; catalytic; for RNase H activity1 Publication1
Metal bindingi1136Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1211Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1263Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1299Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri390 – 407CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri411 – 428CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1150 – 1191Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1370 – 1417Integrase-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionAspartyl protease, DNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein
Biological processActivation of host caspases by virus, DNA integration, DNA recombination, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Modulation of host cell apoptosis by virus, Viral genome integration, Viral penetration into host nucleus, Viral release from host cell, Virion maturation, Virus entry into host cell
LigandLipid-binding, Magnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Alternative name(s):
Pr160Gag-Pol
Cleaved into the following 11 chains:
Matrix protein p17
Short name:
MA
Capsid protein p24
Short name:
CA
Spacer peptide 1By similarity
Short name:
SP1
Alternative name(s):
p2
Nucleocapsid protein p7
Short name:
NC
Transframe peptide
Short name:
TF
p6-pol
Short name:
p6*
Protease (EC:3.4.23.16)
Alternative name(s):
PR
Retropepsin
Reverse transcriptase/ribonuclease H (EC:2.7.7.49, EC:2.7.7.7, EC:3.1.26.13)
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
p66 RT
p51 RT
p15
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiHuman immunodeficiency virus type 1 group M subtype B (isolate LW123) (HIV-1)
Taxonomic identifieri82834 [NCBI]
Taxonomic lineageiViruses › Ortervirales › Retroviridae › Orthoretrovirinae › Lentivirus ›
Virus hostiHomo sapiens (Human) [TaxID: 9606]

Subcellular locationi

Gag-Pol polyprotein :
Matrix protein p17 :
Capsid protein p24 :
Nucleocapsid protein p7 :
Reverse transcriptase/ribonuclease H :
Integrase :

GO - Cellular componenti

View the complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host endosome, Host membrane, Host nucleus, Membrane, Virion

Pathology & Biotechi

Keywords - Diseasei

AIDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostBy similarity
ChainiPRO_00003250282 – 1435Gag-Pol polyproteinBy similarityAdd BLAST1434
ChainiPRO_00003250292 – 132Matrix protein p17By similarityAdd BLAST131
ChainiPRO_0000325030133 – 363Capsid protein p24By similarityAdd BLAST231
PeptideiPRO_0000325031364 – 377Spacer peptide 1By similarityAdd BLAST14
ChainiPRO_0000325032378 – 432Nucleocapsid protein p7By similarityAdd BLAST55
PeptideiPRO_0000325033433 – 440Transframe peptideSequence analysis8
ChainiPRO_0000325034441 – 488p6-polSequence analysisAdd BLAST48
ChainiPRO_0000325035489 – 587ProteaseBy similarityAdd BLAST99
ChainiPRO_0000325036588 – 1147Reverse transcriptase/ribonuclease HBy similarityAdd BLAST560
ChainiPRO_0000325037588 – 1027p51 RTBy similarityAdd BLAST440
ChainiPRO_00003250381028 – 1147p15By similarityAdd BLAST120
ChainiPRO_00003250391148 – 1435IntegraseBy similarityAdd BLAST288

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by hostBy similarity1
Modified residuei132Phosphotyrosine; by hostBy similarity1

Post-translational modificationi

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.PROSITE-ProRule annotationBy similarity
Matrix protein p17: Tyrosine phosphorylated presumably in the virion by a host kinase. Phosphorylation is apparently not a major regulator of membrane association.By similarity
Capsid protein p24: Phosphorylated possibly by host MAPK1; this phosphorylation is necessary for Pin1-mediated virion uncoating.By similarity
Nucleocapsid protein p7: Methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei132 – 133Cleavage; by viral proteaseBy similarity2
Sitei363 – 364Cleavage; by viral proteaseBy similarity2
Sitei377 – 378Cleavage; by viral proteaseBy similarity2
Sitei432 – 433Cleavage; by viral proteaseSequence analysis2
Sitei440 – 441Cleavage; by viral proteaseBy similarity2
Sitei488 – 489Cleavage; by viral proteaseBy similarity2
Sitei587 – 588Cleavage; by viral proteaseBy similarity2
Sitei1027 – 1028Cleavage; by viral protease; partialSequence analysis2
Sitei1147 – 1148Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Proteomic databases

PRIDEiP0C6F2

Interactioni

Subunit structurei

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).By similarity

Structurei

Secondary structure

11435
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0C6F2
SMRiP0C6F2
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C6F2

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini508 – 577Peptidase A2PROSITE-ProRule annotationAdd BLAST70
Domaini631 – 821Reverse transcriptasePROSITE-ProRule annotationAdd BLAST191
Domaini1021 – 1144RNase HPROSITE-ProRule annotationAdd BLAST124
Domaini1201 – 1351Integrase catalyticPROSITE-ProRule annotationAdd BLAST151

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni7 – 31Interaction with Gp41By similarityAdd BLAST25
Regioni8 – 43Interaction with host CALM1By similarityAdd BLAST36
Regioni12 – 19Interaction with host AP3D1By similarity8
Regioni14 – 33Interaction with membrane phosphatidylinositol 4,5-bisphosphate and RNABy similarityAdd BLAST20
Regioni73 – 77Interaction with membrane phosphatidylinositol 4,5-bisphosphateBy similarity5
Regioni189 – 227Interaction with human PPIA/CYPA and NUP153By similarityAdd BLAST39
Regioni277 – 363Dimerization/Multimerization of capsid protein p24By similarityAdd BLAST87
Regioni489 – 493Dimerization of proteaseBy similarity5
Regioni537 – 543Dimerization of proteaseBy similarity7
Regioni576 – 588Dimerization of proteaseBy similarityAdd BLAST13
Regioni814 – 822RT 'primer grip'By similarity9

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi16 – 22Nuclear export signalBy similarity7
Motifi26 – 32Nuclear localization signalBy similarity7
Motifi985 – 1001Tryptophan repeat motifBy similarityAdd BLAST17

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi688 – 691Poly-Lys4

Domaini

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.By similarity
Reverse transcriptase/ribonuclease H: The tryptophan repeat motif is involved in RT p66/p51 dimerization (By similarity).By similarity
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.By similarity

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri390 – 407CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri411 – 428CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1150 – 1191Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Repeat, Zinc-finger

Family and domain databases

CDDicd05482 HIV_retropepsin_like, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.90, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR000721 Gag_p24
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR000071 Lentvrl_matrix_N
IPR012344 Matrix_HIV/RSV_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010659 RVT_connect
IPR010661 RVT_thumb
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00540 Gag_p17, 1 hit
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF00075 RNase_H, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF06815 RVT_connect, 1 hit
PF06817 RVT_thumb, 1 hit
PF00098 zf-CCHC, 2 hits
PRINTSiPR00234 HIV1MATRIX
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF46919 SSF46919, 1 hit
SSF47836 SSF47836, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 2 hits
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS50175 ASP_PROT_RETROV, 1 hit
PS00141 ASP_PROTEASE, 1 hit
PS50994 INTEGRASE, 1 hit
PS51027 INTEGRASE_DBD, 1 hit
PS50879 RNASE_H, 1 hit
PS50878 RT_POL, 1 hit
PS50158 ZF_CCHC, 2 hits
PS50876 ZF_INTEGRASE, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket
Note: 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.
Isoform Gag-Pol polyprotein (identifier: P0C6F2-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MGARASVLSG GKLDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL 
        60         70         80         90        100
LETSEGCRQI LGQLQPSLQT GSEECRSLYN TVATLYCVHQ RIEIKDTKEA 
       110        120        130        140        150
LDKIKEEQNK SKKKAQQAAA DTGHSSQVSQ NYPIVQNIQG QMVHQAISPR 
       160        170        180        190        200
TLNAWVKVVE EKAFSPEVIP MFSALSEGAT PQDLNTMLNT VGGHQAAMQM 
       210        220        230        240        250
LKETINEEAA EWDRVHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM 
       260        270        280        290        300
TNNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK EPFRDYVDRF 
       310        320        330        340        350
YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC 
       360        370        380        390        400
QGVGGPGHKA RVLAEAMSQV TNSATIMMQR GNFRNQRKIV KCFNCGKEGH 
       410        420        430        440        450
IARNCRAPRK KGCWKCGKEG HQMKDCTERQ ANFFREDLAF LQGKAREFSS 
       460        470        480        490        500
EQTRANSPTR RELQVWGRDN NSPSEAGADR QGTVSFNFPQ ITLWQRPLVT 
       510        520        530        540        550
IKIGGQLKEA LLDTGADDTV LEEMSLPGRW KPKMIGGIGG FIKVRQYDQI 
       560        570        580        590        600
LIEICGHKAI GTVLVGPTPV NIIGRNLLTQ IGCTLNFPIS PIETVPVKLK 
       610        620        630        640        650
PGMDGPKVKQ WPLTEEKIKA LVEICTEMEK EGKISKIGPE NPYNTPVFAI 
       660        670        680        690        700
KKKDSTKWRK LVDFRELNKR TQDFWEVQLG IPHPAGLKKK KSVTVLDVGD 
       710        720        730        740        750
AYFSVPLDED FRKYTAFTIP SINNETPGIR YQYNVLPQGW KGSPAIFQSS 
       760        770        780        790        800
MTKILEPFRK QNPDIVIYQY MDDLYVGSDL EIGQHRTKIE ELRQHLLRWG 
       810        820        830        840        850
LTTPDKKHQK EPPFLWMGYE LHPDKWTVQP IVLPEKDSWT VNDIQKLVGK 
       860        870        880        890        900
LNWASQIYPG IKVRQLCKLL RGTKALTEVI PLTEEAELEL AENREILKEP 
       910        920        930        940        950
VHGVYYDPSK DLIAEIQKQG QGQWTYQIYQ EPFKNLKTGK YARMRGTHTN 
       960        970        980        990       1000
DVKQLTEAVQ KITTESIVIW GKTPKFKLPI QKETWETWWT EYWQATWIPE 
      1010       1020       1030       1040       1050
WEFVNTPPLV KLWYQLEKEP IVGAETFYVD GAANRETKLG KAGYVTNKGR 
      1060       1070       1080       1090       1100
QKVVPLTNTT NQKTELQAIY LALQDSGLEV NIVTDSQYAL GIIQAQPDKS 
      1110       1120       1130       1140       1150
ESELVNQIIE QLIKKEKVYL AWVPAHKGIG GNEQVDKLVS AGIRKILFLD 
      1160       1170       1180       1190       1200
GIDKAQDEHE KYHSNWRAMA SDFNLPPVVA KEIVASCDKC QLKGEAMHGQ 
      1210       1220       1230       1240       1250
VDCSPGIWQL DCTHLEGKVI LVAVHVASGY IEAEVIPAET GQETAYFLLK 
      1260       1270       1280       1290       1300
LAGRWPVKTI HTDNGSNFTS ATVKAACWWA GIKQEFGIPY NPQSQGVVES 
      1310       1320       1330       1340       1350
MNKELKKIIG QVRDQAEHLK TAVQMAVFIH NFKRKGGIGG YSAGERIVDI 
      1360       1370       1380       1390       1400
IATDIQTKEL QKQITKIQNF RVYYRDSRNP LWKGPAKLLW KGEGAVVIQD 
      1410       1420       1430 
NSDIKVVPRR KAKIIRDYGK QMAGDDCVAS RQDED
Note: Produced by -1 ribosomal frameshifting.
Length:1,435
Mass (Da):162,076
Last modified:March 18, 2008 - v1
Checksum:i36226C1CBDB26464
GO
Isoform Gag polyprotein (identifier: Q70622-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry Q70622.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:500
Mass (Da):55,903
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U12055 Genomic RNA No translation available.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Similar proteinsi

Cross-referencesi

Web resourcesi

HIV drug resistance mutations
hivdb

HIV drug resistance database

BioAfrica: HIV bioinformatics in Africa

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U12055 Genomic RNA No translation available.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LP3X-ray2.80A/B1014-1149[»]
3TH9X-ray1.34A/B489-587[»]
3VFAX-ray1.43A/B489-587[»]
4I8WX-ray1.96A/B489-587[»]
4I8ZX-ray1.75A/B489-587[»]
4MC1X-ray1.39A/B489-587[»]
4MC2X-ray1.56A/B489-587[»]
4MC6X-ray1.31A/B489-587[»]
4MC9X-ray1.19A/B489-587[»]
4NYFX-ray1.90A/B1199-1357[»]
4QGIX-ray1.90A/B489-587[»]
5K14X-ray2.40B588-1027[»]
ProteinModelPortaliP0C6F2
SMRiP0C6F2
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP0C6F2

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP0C6F2
PROiPR:P0C6F2

Family and domain databases

CDDicd05482 HIV_retropepsin_like, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.90, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR000721 Gag_p24
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR000071 Lentvrl_matrix_N
IPR012344 Matrix_HIV/RSV_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010659 RVT_connect
IPR010661 RVT_thumb
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00540 Gag_p17, 1 hit
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF00075 RNase_H, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF06815 RVT_connect, 1 hit
PF06817 RVT_thumb, 1 hit
PF00098 zf-CCHC, 2 hits
PRINTSiPR00234 HIV1MATRIX
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF46919 SSF46919, 1 hit
SSF47836 SSF47836, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 2 hits
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS50175 ASP_PROT_RETROV, 1 hit
PS00141 ASP_PROTEASE, 1 hit
PS50994 INTEGRASE, 1 hit
PS51027 INTEGRASE_DBD, 1 hit
PS50879 RNASE_H, 1 hit
PS50878 RT_POL, 1 hit
PS50158 ZF_CCHC, 2 hits
PS50876 ZF_INTEGRASE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPOL_HV1LW
AccessioniPrimary (citable) accession number: P0C6F2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 18, 2008
Last sequence update: March 18, 2008
Last modified: September 12, 2018
This is version 85 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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