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P05896

- POL_SIVM1

UniProt

P05896 - POL_SIVM1

Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Simian immunodeficiency virus (isolate Mm142-83) (SIV-mac) (Simian immunodeficiency virus rhesus monkey)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 137 (01 Oct 2014)
      Sequence version 2 (02 Oct 2007)
      Previous versions | rss
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    Functioni

    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.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 myristointegration complex. The myristoylation signal and the NLS 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.By similarity
    Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry. Interaction with host PPIA/CYPA protects the virus from restriction by host TRIM5-alpha and from an unknown antiviral activity in host cells. This capsid restriction by TRIM5 is one of the factors which restricts SIV to the simian species By similarity.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.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.PROSITE-ProRule annotation
    Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral dimeric 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 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 can probably 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.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 SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration By similarity.By similarity

    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.
    3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation

    Cofactori

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

    Enzyme regulationi

    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.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei135 – 1362Cleavage; by viral proteaseBy similarity
    Sitei364 – 3652Cleavage; by viral proteaseBy similarity
    Sitei433 – 4342Cleavage; by viral proteaseBy similarity
    Sitei500 – 5012Cleavage; by viral proteaseBy similarity
    Active sitei522 – 5221For protease activity; shared with dimeric partnerPROSITE-ProRule annotation
    Sitei596 – 5972Cleavage; by viral proteaseBy similarity
    Metal bindingi706 – 7061Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi781 – 7811Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi782 – 7821Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Sitei996 – 9961Essential for RT p66/p51 heterodimerizationBy similarity
    Sitei1009 – 10091Essential for RT p66/p51 heterodimerizationBy similarity
    Sitei1035 – 10362Cleavage; by viral proteaseBy similarity
    Metal bindingi1038 – 10381Magnesium; catalytic; for RNase H activityBy similarity
    Metal bindingi1073 – 10731Magnesium; catalytic; for RNase H activityBy similarity
    Metal bindingi1093 – 10931Magnesium; catalytic; for RNase H activityBy similarity
    Metal bindingi1144 – 11441Magnesium; catalytic; for RNase H activityBy similarity
    Sitei1155 – 11562Cleavage; by viral proteaseBy similarity
    Metal bindingi1219 – 12191Magnesium; catalytic; for integrase activityBy similarity
    Metal bindingi1271 – 12711Magnesium; catalytic; for integrase activityBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri391 – 40818CCHC-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri412 – 42918CCHC-type 2PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri1158 – 119942Integrase-typePROSITE-ProRule annotationAdd
    BLAST
    DNA bindingi1378 – 142548Integrase-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: UniProtKB-KW
    2. DNA binding Source: UniProtKB-KW
    3. DNA-directed DNA polymerase activity Source: UniProtKB-KW
    4. exoribonuclease H activity Source: UniProtKB-EC
    5. RNA binding Source: UniProtKB-KW
    6. RNA-directed DNA polymerase activity Source: UniProtKB-KW
    7. RNA-DNA hybrid ribonuclease activity Source: InterPro
    8. structural molecule activity Source: InterPro
    9. zinc ion binding Source: InterPro

    GO - Biological processi

    1. DNA integration Source: UniProtKB-KW
    2. DNA recombination Source: UniProtKB-KW
    3. establishment of integrated proviral latency Source: UniProtKB-KW
    4. suppression by virus of host gene expression Source: UniProtKB-KW
    5. viral entry into host cell Source: UniProtKB-KW
    6. viral penetration into host nucleus Source: UniProtKB-KW
    7. viral release from host cell Source: UniProtKB-KW

    Keywords - Molecular functioni

    Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

    Keywords - Biological processi

    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, Viral genome integration, Viral penetration into host nucleus, Virion maturation, Virus entry into host cell, Virus exit from host cell

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Gag-Pol polyprotein
    Alternative name(s):
    Pr160Gag-Pol
    Cleaved into the following 9 chains:
    Matrix protein p17
    Short name:
    MA
    Capsid protein p24
    Short name:
    CA
    p6-pol
    Short name:
    p6*
    Alternative name(s):
    PR
    Retropepsin
    Alternative name(s):
    Exoribonuclease H (EC:3.1.13.2)
    p66 RT
    Integrase
    Short name:
    IN
    Gene namesi
    Name:gag-pol
    OrganismiSimian immunodeficiency virus (isolate Mm142-83) (SIV-mac) (Simian immunodeficiency virus rhesus monkey)
    Taxonomic identifieri11733 [NCBI]
    Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
    Virus hostiCercopithecidae (Old World monkeys) [TaxID: 9527]
    ProteomesiUP000007220: Genome

    Subcellular locationi

    Chain Matrix protein p17 : Virion Curated. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane Curated; Lipid-anchor Curated
    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.By similarity
    Chain Integrase : Virion Curated. Host nucleus Curated. Host cytoplasm Curated
    Note: Nuclear at initial phase, cytoplasmic at assembly.Curated

    GO - Cellular componenti

    1. host cell cytoplasm Source: UniProtKB-SubCell
    2. host cell nucleus Source: UniProtKB-SubCell
    3. host cell plasma membrane Source: UniProtKB-SubCell
    4. intracellular Source: GOC
    5. membrane Source: UniProtKB-KW
    6. viral nucleocapsid Source: UniProtKB-KW

    Keywords - Cellular componenti

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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed; by hostBy similarity
    Chaini2 – 14481447Gag-Pol polyproteinPRO_0000306035Add
    BLAST
    Chaini2 – 135134Matrix protein p17By similarityPRO_0000306036Add
    BLAST
    Chaini136 – 364229Capsid protein p24By similarityPRO_0000306037Add
    BLAST
    Chaini365 – 43369Nucleocapsid protein p7By similarityPRO_0000306038Add
    BLAST
    Chaini434 – 50067p6-polSequence AnalysisPRO_0000306039Add
    BLAST
    Chaini501 – 59696ProteaseBy similarityPRO_0000306040Add
    BLAST
    Chaini597 – 1155559Reverse transcriptase/ribonuclease HBy similarityPRO_0000306041Add
    BLAST
    Chaini597 – 1035439p51 RTBy similarityPRO_0000306042Add
    BLAST
    Chaini1036 – 1155120p15By similarityPRO_0000306043Add
    BLAST
    Chaini1156 – 1448293IntegraseBy similarityPRO_0000306044Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity

    Post-translational modificationi

    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.PROSITE-ProRule annotation
    Capsid protein p24 is phosphorylated.

    Keywords - PTMi

    Lipoprotein, Myristate, Phosphoprotein

    Interactioni

    Subunit structurei

    Matrix protein p17 is a trimer. Interacts with gp120. 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. The integrase is a homodimer and possibly a homotetramer By similarity.By similarity

    Structurei

    Secondary structure

    1
    1448
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi502 – 5043
    Beta strandi507 – 5126
    Beta strandi515 – 5217
    Beta strandi525 – 5273
    Beta strandi540 – 5445
    Beta strandi551 – 56313
    Beta strandi566 – 57510
    Helixi584 – 5896
    Beta strandi593 – 5953
    Beta strandi1215 – 12239
    Beta strandi1226 – 12327
    Beta strandi1239 – 12435
    Helixi1249 – 126012
    Beta strandi1267 – 12693
    Helixi1280 – 12889
    Beta strandi1291 – 12933
    Turni1309 – 13113
    Helixi1312 – 13187
    Turni1319 – 13224
    Beta strandi1323 – 13253
    Helixi1327 – 133913
    Beta strandi1344 – 13474
    Helixi1351 – 136313

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AZ5X-ray2.00A498-595[»]
    1C6VX-ray3.00A/B/C/D1205-1368[»]
    1SIVX-ray2.50A/B498-596[»]
    1TCWX-ray2.40A/B498-596[»]
    1YTIX-ray2.20A498-595[»]
    1YTJX-ray2.50A498-595[»]
    ProteinModelPortaliP05896.
    SMRiP05896. Positions 2-135, 146-352, 383-432, 498-596, 599-1151, 1156-1201, 1210-1368, 1371-1425.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP05896.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini517 – 58670Peptidase A2PROSITE-ProRule annotationAdd
    BLAST
    Domaini640 – 830191Reverse transcriptasePROSITE-ProRule annotationAdd
    BLAST
    Domaini1029 – 1152124RNase HPROSITE-ProRule annotationAdd
    BLAST
    Domaini1209 – 1359151Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni823 – 8319RT 'primer grip'By similarity

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi16 – 227Nuclear export signalBy similarity
    Motifi26 – 327Nuclear localization signalBy similarity
    Motifi993 – 100917Tryptophan repeat motifBy similarityAdd
    BLAST

    Domaini

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

    Sequence similaritiesi

    Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
    Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
    Contains 1 integrase-type DNA-binding domain.PROSITE-ProRule annotation
    Contains 1 integrase-type zinc finger.PROSITE-ProRule annotation
    Contains 1 peptidase A2 domain.PROSITE-ProRule annotation
    Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
    Contains 1 RNase H domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri391 – 40818CCHC-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri412 – 42918CCHC-type 2PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri1158 – 119942Integrase-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Family and domain databases

    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.
    4.10.60.10. 1 hit.
    InterProiIPR001969. 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]
    PfamiPF00540. 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]
    PRINTSiPR00234. HIV1MATRIX.
    SMARTiSM00343. ZnF_C2HC. 2 hits.
    [Graphical view]
    SUPFAMiSSF46919. 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.
    PROSITEiPS50175. 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]

    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. Align

    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: P05896-1) [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

    MGARNSVLSG KKADELEKIR LRPGGKKKYM LKHVVWAANE LDRFGLAESL     50
    LENKEGCQKI LSVLAPLVPT GSENLKSLYN TVCVIWCIHA EEKVKHTEEA 100
    KQIVQRHLVM ETGTAETMPK TSRPTAPFSG RGGNYPVQQI GGNYTHLPLS 150
    PRTLNAWVKL IEEKKFGAEV VSGFQALSEG CLPYDINQML NCVGDHQAAM 200
    QIIRDIINEE AADWDLQHPQ QAPQQGQLRE PSGSDIAGTT STVEEQIQWM 250
    YRQQNPIPVG NIYRRWIQLG LQKCVRMYNP TNILDVKQGP KEPFQSYVDR 300
    FYKSLRAEQT DPAVKNWMTQ TLLIQNANPD CKLVLKGLGT NPTLEEMLTA 350
    CQGVGGPGQK ARLMAEALKE ALAPAPIPFA AAQQKGPRKP IKCWNCGKEG 400
    HSARQCRAPR RQGCWKCGKM DHVMAKCPNR QAGFFRPWPL GKEAPQFPHG 450
    SSASGADANC SPRRTSCGSA KELHALGQAA ERKQREALQG GDRGFAAPQF 500
    SLWRRPVVTA HIEGQPVEVL LDTGADDSIV TGIELGPHYT PKIVGGIGGF 550
    INTKEYKNVE IEVLGKRIKG TIMTGDTPIN IFGRNLLTAL GMSLNLPIAK 600
    VEPVKSPLKP GKDGPKLKQW PLSKEKIVAL REICEKMEKD GQLEEAPPTN 650
    PYNTPTFAIK KKDKNKWRML IDFRELNRVT QDFTEVQLGI PHPAGLAKRK 700
    RITVLDIGDA YFSIPLDEEF RQYTAFTLPS VNNAEPGKRY IYKVLPQGWK 750
    GSPAIFQYTM RHVLEPFRKA NPDVTLVQYM DDILIASDRT DLEHDRVVLQ 800
    LKELLNSIGF SSPEEKFQKD PPFQWMGYEL WPTKWKLQKI ELPQRETWTV 850
    NDIQKLVGVL NWAAQIYPGI KTKHLCRLIR GKMTLTEEVQ WTEMAEAEYE 900
    ENKIILSQEQ EGCYYQESKP LEATVIKSQD NQWSYKIHQE DKILKVGKFA 950
    KIKNTHTNGV RLLAHVIQKI GKEAIVIWGQ VPKFHLPVEK DVWEQWWTDY 1000
    WQVTWIPEWD FISTPPLVRL VFNLVKDPIE GEETYYVDGS CSKQSKEGKA 1050
    GYITDRGKDK VKVLEQTTNQ QAELEAFLMA LTDSGPKANI IVDSQYVMGI 1100
    ITGCPTESES RLVNQIIEEM IKKTEIYVAW VPAHKGIGGN QEIDHLVSQG 1150
    IRQVLFLEKI EPAQEEHSKY HSNIKELVFK FGLPRLVAKQ IVDTCDKCHQ 1200
    KGEAIHGQVN SDLGTWQMDC THLEGKIVIV AVHVASGFIE AEVIPQETGR 1250
    QTALFLLKLA SRWPITHLHT DNGANFASQE VKMVAWWAGI EHTFGVPYNP 1300
    QSQGVVEAMN HHLKNQIDRI REQANSVETI VLMAVHCMNF KRRGGIGDMT 1350
    PAERLINMIT TEQEIQFQQS KNSKFKNFRV YYREGRDQLW KGPGELLWKG 1400
    EGAVILKVGT DIKVVPRRKA KIIKDYGGGK EMDSSSHMED TGEAREVA 1448

    Note: Produced by -1 ribosomal frameshifting.

    Length:1,448
    Mass (Da):163,372
    Last modified:October 2, 2007 - v2
    Checksum:i460D13331B3E68E5
    GO
    Isoform Gag polyprotein (identifier: P05894-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry P05894.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by conventional translation.

    Length:506
    Mass (Da):56,436
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y00277 Genomic DNA. Translation: CAA68380.1.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y00277 Genomic DNA. Translation: CAA68380.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AZ5 X-ray 2.00 A 498-595 [» ]
    1C6V X-ray 3.00 A/B/C/D 1205-1368 [» ]
    1SIV X-ray 2.50 A/B 498-596 [» ]
    1TCW X-ray 2.40 A/B 498-596 [» ]
    1YTI X-ray 2.20 A 498-595 [» ]
    1YTJ X-ray 2.50 A 498-595 [» ]
    ProteinModelPortali P05896.
    SMRi P05896. Positions 2-135, 146-352, 383-432, 498-596, 599-1151, 1156-1201, 1210-1368, 1371-1425.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P05896.

    Family and domain databases

    Gene3Di 1.10.10.200. 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.
    InterProi IPR001969. 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 ]
    Pfami 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.
    [Graphical view ]
    PRINTSi PR00234. HIV1MATRIX.
    SMARTi SM00343. ZnF_C2HC. 2 hits.
    [Graphical view ]
    SUPFAMi SSF46919. 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.
    PROSITEi 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.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence of simian immunodeficiency virus from macaque and its relationship to other human and simian retroviruses."
      Chakrabarti L., Guyader M., Alizon M., Daniel M.D., Desrosiers R.C., Tiollais P., Sonigo P.
      Nature 328:543-547(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Domain flexibility in retroviral proteases: structural implications for drug resistant mutations."
      Rose R.B., Craik C.S., Stroud R.M.
      Biochemistry 37:2607-2621(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 498-595.

    Entry informationi

    Entry nameiPOL_SIVM1
    AccessioniPrimary (citable) accession number: P05896
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1988
    Last sequence update: October 2, 2007
    Last modified: October 1, 2014
    This is version 137 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    This is a macaque isolate.
    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.

    Keywords - Technical termi

    3D-structure, Complete proteome, Multifunctional enzyme

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3