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P24740 (POL_HV1U4) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 148. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Gag-Pol polyprotein
Alternative name(s):
Pr160Gag-Pol

Cleaved into the following 11 chains:

  1. Matrix protein p17
    Short name=MA
  2. Capsid protein p24
    Short name=CA
  3. Spacer peptide p2
  4. Nucleocapsid protein p7
    Short name=NC
  5. Transframe peptide
    Short name=TF
  6. p6-pol
    Short name=p6*
  7. Protease
    EC=3.4.23.16
    Alternative name(s):
    PR
    Retropepsin
  8. 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
  9. p51 RT
  10. p15
  11. Integrase
    Short name=IN
Gene names
Name:gag-pol
OrganismHuman immunodeficiency virus type 1 group M subtype A (isolate U455) (HIV-1)
Taxonomic identifier11703 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length1428 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation By similarity.

Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to play a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu 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. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species By similarity.

Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity By similarity.

The aspartyl protease 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.

Reverse transcriptase/ribonuclease H (RT) is a 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 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.

Catalytic activity

Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

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.

3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactor

Binds 2 magnesium ions for reverse transcriptase polymerase activity By similarity.

Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding By similarity.

Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions By similarity.

Enzyme regulation

The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir. 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. Use of protease inhibitors in tritherapy regimens permit more ambitious therapeutic strategies By similarity.

Subunit structure

Pre-integration complex interacts with human HMGA1. Matrix protein p17 is a trimer. Interacts with gp120 and human BAF. Capsid is a homodimer. Interacts with human PPIA/CYPA. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a 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 is a homodimer and possibly can form homotetramer. Integrase interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1Integrase interacts with human KPNA3; this interaction might play a role in nuclear import of the pre-integration complex. Integrase interacts with human NUP153; this interaction might play a role in nuclear import of the pre-integration complex By similarity.

Subcellular location

Matrix protein p17: Virion Potential. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane; Lipid-anchor Potential. Note: Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane By similarity.

Capsid protein p24: Virion Potential.

Nucleocapsid protein p7: Virion Potential.

Reverse transcriptase/ribonuclease H: Virion Potential.

Integrase: Virion Potential. Host nucleus Potential. Host cytoplasm Potential. Note: Nuclear at initial phase, cytoplasmic at assembly Potential.

Domain

The 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.

The tryptophan repeat motif is involved in RT p66/p51 dimerization By similarity.

Integrase 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,D35E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.

Post-translational modification

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 By similarity.

Capsid protein p24 is phosphorylated By similarity.

Matrix protein p17 is tyrosine phosphorylated presumably in the virion by a host kinase. This modification targets the matrix protein to the nucleus By similarity.

Miscellaneous

Capsid protein p24 is able to bind macaque TRIM5-alpha or owl monkey TRIMCyp, preventing reverse transcription of the viral genome and succesfull infection of macaque or owl monkey by HIV-1 By similarity.

The reverse transcriptase is an 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.

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).

Sequence similarities

Contains 2 CCHC-type zinc fingers.

Contains 1 integrase catalytic domain.

Contains 1 integrase-type DNA-binding domain.

Contains 1 integrase-type zinc finger.

Contains 1 peptidase A2 domain.

Contains 1 reverse transcriptase domain.

Contains 1 RNase H domain.

Ontologies

Keywords
   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
Virion maturation
Virus entry into host cell
Virus exit from host cell
   Cellular componentCapsid protein
Host cell membrane
Host cytoplasm
Host membrane
Host nucleus
Membrane
Virion
   Coding sequence diversityRibosomal frameshifting
   DiseaseAIDS
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Magnesium
Metal-binding
RNA-binding
Viral nucleoprotein
Zinc
   Molecular functionAspartyl protease
DNA-directed DNA polymerase
Endonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Protease
RNA-directed DNA polymerase
Transferase
   PTMLipoprotein
Myristate
Phosphoprotein
   Technical term3D-structure
Multifunctional enzyme
Gene Ontology (GO)
   Biological_processDNA integration

Inferred from electronic annotation. Source: UniProtKB-KW

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

establishment of integrated proviral latency

Inferred from electronic annotation. Source: UniProtKB-KW

induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host translation

Inferred from electronic annotation. Source: UniProtKB-KW

viral entry into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

viral penetration into host nucleus

Inferred from electronic annotation. Source: UniProtKB-KW

viral release from host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componenthost cell cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

intracellular

Inferred from electronic annotation. Source: GOC

membrane

Inferred from electronic annotation. Source: UniProtKB-KW

viral nucleocapsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-directed DNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA-DNA hybrid ribonuclease activity

Inferred from electronic annotation. Source: InterPro

RNA-directed DNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

aspartic-type endopeptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

exoribonuclease H activity

Inferred from electronic annotation. Source: UniProtKB-EC

structural molecule activity

Inferred from electronic annotation. Source: InterPro

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

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: P24740-1)

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.
Note: Produced by -1 ribosomal frameshifting.
Isoform Gag polyprotein (identifier: P24736-1)

The sequence of this isoform can be found in the external entry P24736.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 14281427Gag-Pol polyprotein
PRO_0000261282
Chain2 – 128127Matrix protein p17 By similarity
PRO_0000042430
Chain129 – 359231Capsid protein p24 By similarity
PRO_0000042431
Peptide360 – 37112Spacer peptide p2 By similarity
PRO_0000042432
Chain372 – 42655Nucleocapsid protein p7 By similarity
PRO_0000042433
Peptide427 – 4348Transframe peptide Potential
PRO_0000246732
Chain435 – 48147p6-pol Potential
PRO_0000042434
Chain482 – 58099Protease By similarity
PRO_0000038664
Chain581 – 1140560Reverse transcriptase/ribonuclease H By similarity
PRO_0000042435
Chain581 – 1020440p51 RT By similarity
PRO_0000042436
Chain1021 – 1140120p15 By similarity
PRO_0000042437
Chain1141 – 1428288Integrase By similarity
PRO_0000042438

Regions

Domain501 – 57070Peptidase A2
Domain624 – 814191Reverse transcriptase
Domain1014 – 1137124RNase H
Domain1194 – 1344151Integrase catalytic
Zinc finger384 – 40118CCHC-type 1
Zinc finger405 – 42218CCHC-type 2
Zinc finger1143 – 118442Integrase-type
DNA binding1363 – 141048Integrase-type
Region807 – 8159RT 'primer grip' By similarity
Motif16 – 227Nuclear export signal By similarity
Motif26 – 327Nuclear localization signal By similarity
Motif978 – 99417Tryptophan repeat motif By similarity

Sites

Active site5061For protease activity; shared with dimeric partner By similarity
Metal binding6901Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding7651Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding7661Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding10231Magnesium; catalytic; for RNase H activity By similarity
Metal binding10581Magnesium; catalytic; for RNase H activity By similarity
Metal binding10781Magnesium; catalytic; for RNase H activity By similarity
Metal binding11291Magnesium; catalytic; for RNase H activity By similarity
Metal binding12041Magnesium; catalytic; for integrase activity By similarity
Metal binding12561Magnesium; catalytic; for integrase activity By similarity
Site128 – 1292Cleavage; by viral protease By similarity
Site217 – 2182Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA By similarity
Site359 – 3602Cleavage; by viral protease By similarity
Site371 – 3722Cleavage; by viral protease By similarity
Site426 – 4272Cleavage; by viral protease Potential
Site434 – 4352Cleavage; by viral protease By similarity
Site481 – 4822Cleavage; by viral protease By similarity
Site580 – 5812Cleavage; by viral protease By similarity
Site9811Essential for RT p66/p51 heterodimerization By similarity
Site9941Essential for RT p66/p51 heterodimerization By similarity
Site1020 – 10212Cleavage; by viral protease; partial By similarity
Site1140 – 11412Cleavage; by viral protease By similarity

Amino acid modifications

Modified residue1281Phosphotyrosine; by host By similarity
Lipidation21N-myristoyl glycine; by host By similarity

Secondary structure

...................... 1428
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Gag-Pol polyprotein [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: E98527B81D866C0C

FASTA1,428161,103
        10         20         30         40         50         60 
MGARASVLSG KKLDSWEKIR LRPGGNKKYR LKHLVWASRE LEKFTLNPGL LETAEGCQQI 

        70         80         90        100        110        120 
LGQLQPALQT GTEELRSLYN TVAVLYCVHQ RIDVKDTKEA LNKIEEMQNK NKQRTQQAAA 

       130        140        150        160        170        180 
NTGSSQNYPI VQNAQGQPVH QALSPRTLNA WVKVVEDKAF SPEVIPMFSA LSEGATPQDL 

       190        200        210        220        230        240 
NMMLNVVGGH QAAMQMLKDT INEEAAEWDR LHPVHAGPIP PGQMREPRGS DIAGTTSTVQ 

       250        260        270        280        290        300 
EQIGWMTGNP PIPVGDIYRR WIILGLNKIV RMYSPVSILD IRQGPKEPFR DYVDRFFKTL 

       310        320        330        340        350        360 
RAEQATQDVK NWMTETLLVQ NANPDCKSIL RALGPGATLE EMMTACQGVG GPGHKARVLA 

       370        380        390        400        410        420 
EAMSQVQQTS IMMQRGNFRG PRRIKCFNCG KEGHLAKNCR APRKKGCWKC GKEGHQMKDC 

       430        440        450        460        470        480 
TERQANFLRE NLAFQQGEAR EFSSEQTRAN SPTSRNLWDG GKDDLPCETG AERQGTDSFS 

       490        500        510        520        530        540 
FPQITLWQRP LVTVKIGGQL IEALLDTGAD DTVLEDINLP GKWKPKIIGG IGGFIKVRQY 

       550        560        570        580        590        600 
DQILIEICGK KTIGTVLVGP TPVNIIGRNM LTQIGCTLNF PISPIETVPV KLKPEMDGPK 

       610        620        630        640        650        660 
VKQWPLTEEK IKALTEICNE MEKEGKISKI GPENPYNTPV FAIKKKDSTK WRKLVDFREL 

       670        680        690        700        710        720 
NKRTQDFWEV QLGIPHTAGL KKKKSVTVLD VGDAYFSVPL DESFRKYTAF TIPSINNETP 

       730        740        750        760        770        780 
GVRYQYNVLP QGWKGSPSIF QSSMTKILEP FRSQHPDIVI YQYMDDLYVG SDLEIGQHRA 

       790        800        810        820        830        840 
KIEELRAHLL SWGFITPDKK HQKEPPFLWM GYELHPDKWT VQPIQLPEKD SWTVNDIQKL 

       850        860        870        880        890        900 
VGKLNWASQI YAGIKVKQLC KLLRGAKALT DIVTLTEEAE LELAENREIL KDPVHGVYYD 

       910        920        930        940        950        960 
PSKDLVAEIQ KQGQDQWTYQ IYQEPFKNLK TGKYARKRSA HTNDVKQLTE VVQKVSTESI 

       970        980        990       1000       1010       1020 
VIWGKIPKFR LPIQKETWEA WWMEYWQATW IPEWEFVNTP PLVKLWYQLE KDPIAGAETF 

      1030       1040       1050       1060       1070       1080 
YVDGAANRET KLGKAGYVTD RGRQKVVSLT ETTNQKTELH AIHLALQDSG SEVNIVTDSQ 

      1090       1100       1110       1120       1130       1140 
YALGIIQAQP DRSESEIVNQ IIEKLIEKEK VYLSWVPAHK GIGGNEQVDK LVSSGIRKVL 

      1150       1160       1170       1180       1190       1200 
FLDGIDKAQE DHEKYHCNWR AMASDFNLPP VVAKEIVASC NKCQLKGEAM HGQVDCSPGI 

      1210       1220       1230       1240       1250       1260 
WQLDCTHLEG KVILVAVHVA SGYIEAEVIP AETGQETAYF ILKLAGRWPV KVIHTDNGSN 

      1270       1280       1290       1300       1310       1320 
FTSAAVKAVC WWANIQQEFG IPYNPQSQGV VESMNKELKK IIGQVREQAE HLKTAVQMAV 

      1330       1340       1350       1360       1370       1380 
FIHNFKRKGG IGGYSAGERI IDIIATDIQT KELQKQISKI QNFRVYYRDS RDPIWKGPAK 

      1390       1400       1410       1420 
LLWKGEGAVV IQDNSDIKVV PRRKAKIIRD YGKQMAGDDC MAGRQDED 

« Hide

Isoform Gag polyprotein [UniParc].

See P24736.

References

[1]"Nucleotide sequence of a Ugandan HIV-1 provirus reveals genetic diversity from other HIV-1 isolates."
Oram J.D., Downing R.G., Roff M., Clegg J.C.S., Serwadda D., Carswell J.W.
AIDS Res. Hum. Retroviruses 6:1073-1078(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Proteolytic processing and particle maturation."
Vogt V.M.
Curr. Top. Microbiol. Immunol. 214:95-131(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[3]"Structural biology of HIV."
Turner B.G., Summers M.F.
J. Mol. Biol. 285:1-32(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[4]"Mechanisms of retroviral recombination."
Negroni M., Buc H.
Annu. Rev. Genet. 35:275-302(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[5]"Retroviral proteases."
Dunn B.M., Goodenow M.M., Gustchina A., Wlodawer A.
Genome Biol. 3:REVIEWS3006.1-REVIEWS3006.7(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[6]"Role of HIV-1 Gag domains in viral assembly."
Scarlata S., Carter C.
Biochim. Biophys. Acta 1614:62-72(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[7]"Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy."
Omichinski J.G., Clore G.M., Sakaguchi K., Appella E., Gronenborn A.M.
FEBS Lett. 292:25-30(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 405-422.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M62320 Genomic DNA. Translation: AAA75019.1. Sequence problems.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1E27X-ray2.20C1168-1176[»]
1NCPNMR-C405-422[»]
3LZSX-ray1.95A/B482-580[»]
3LZUX-ray1.76A/B482-580[»]
ProteinModelPortalP24740.
SMRP24740. Positions 2-426, 482-1137, 1141-1410.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.10.10.200. 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.
4.10.60.10. 1 hit.
InterProIPR001969. Aspartic_peptidase_AS.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_N_HIV/RSV.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamPF00540. 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.
[Graphical view]
PRINTSPR00234. HIV1MATRIX.
SMARTSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 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.
PROSITEPS50175. 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.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP24740.

Entry information

Entry namePOL_HV1U4
AccessionPrimary (citable) accession number: P24740
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 148 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references