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Q9TTC1

- POL_KORV

UniProt

Q9TTC1 - POL_KORV

Protein

Pro-Pol polyprotein

Gene

pro-pol

Organism
Koala retrovirus (KoRV)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 78 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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 a polypurine tract (PPT) 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 PPT that has not been removed by RNase H as primer. PPT 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, 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. In the second step, the PIC access cell chromosomes during cell division. 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 (see above) are filled in and then ligated By similarity.By similarity

    Catalytic activityi

    Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation
    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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi229 – 2291Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi303 – 3031Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi304 – 3041Magnesium; catalytic; for reverse transcriptase activityBy similarity
    Metal bindingi661 – 6611Magnesium; catalytic; for RNase H activityBy similarity
    Metal bindingi731 – 7311Magnesium; catalytic; for RNase H activityBy similarity
    Sitei?742 – ?7432Cleavage; by viral proteaseBy similarity
    Metal bindingi904 – 9041Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: UniProtKB-KW
    2. DNA-directed DNA polymerase activity Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. RNA binding Source: UniProtKB-KW
    5. RNA-directed DNA polymerase activity Source: UniProtKB-KW
    6. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

    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. viral entry into 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, Viral genome integration, Virus entry into host cell

    Keywords - Ligandi

    Magnesium, Metal-binding, RNA-binding

    Protein family/group databases

    MEROPSiA02.020.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pro-Pol polyprotein
    Alternative name(s):
    Pr125Pol
    Cleaved into the following 2 chains:
    Alternative name(s):
    p87Pro-RT-RNaseH
    Integrase
    Short name:
    IN
    Alternative name(s):
    p42In
    Gene namesi
    Name:pro-pol
    OrganismiKoala retrovirus (KoRV)
    Taxonomic identifieri394239 [NCBI]
    Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeGammaretrovirusunclassified Gammaretrovirus
    Virus hostiPhascolarctos cinereus (Koala) [TaxID: 38626]
    ProteomesiUP000007765: Genome

    Subcellular locationi

    Chain Integrase : Virion Curated. Host nucleus By similarity. Host cytoplasm Curated
    Note: Nuclear at initial phase, cytoplasmic at assembly.Curated
    Chain Protease/Reverse transcriptase/ribonuclease H : Host nucleus By similarity. 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. virion Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Host cytoplasm, Host nucleus, Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11271127Pro-Pol polyproteinPRO_0000249431Add
    BLAST
    Chaini1 – ?742742Protease/Reverse transcriptase/ribonuclease HBy similarityPRO_0000249432Add
    BLAST
    Chaini?743 – 1127385IntegraseBy similarityPRO_0000249433Add
    BLAST

    Post-translational modificationi

    Specific enzymatic cleavages in vivo by viral protease yield mature proteins. The protease is not cleaved off from Pol. Since cleavage efficiency is not optimal for all sites, long and active p65Pro-RT, p87Pro-RT-RNaseH and even some Pr125Pol are detected in infected cells By similarity.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ9TTC1.
    SMRiQ9TTC1. Positions 103-552, 583-738.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini22 – 9271Peptidase A2PROSITE-ProRule annotationAdd
    BLAST
    Domaini202 – 393192Reverse transcriptasePROSITE-ProRule annotationAdd
    BLAST
    Domaini635 – 781147RNase HPROSITE-ProRule annotationAdd
    BLAST
    Domaini905 – 1063159Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    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.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,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.By similarity

    Sequence similaritiesi

    Contains 1 integrase catalytic domain.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

    Family and domain databases

    Gene3Di3.30.420.10. 2 hits.
    InterProiIPR001584. Integrase_cat-core.
    IPR018061. Pept_A2A_retrovirus_sg.
    IPR001995. Peptidase_A2_cat.
    IPR021109. Peptidase_aspartic_dom.
    IPR012337. RNaseH-like_dom.
    IPR002156. RNaseH_domain.
    IPR000477. RT_dom.
    [Graphical view]
    PfamiPF00075. RNase_H. 1 hit.
    PF00665. rve. 1 hit.
    PF00077. RVP. 1 hit.
    PF00078. RVT_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50630. SSF50630. 1 hit.
    SSF53098. SSF53098. 2 hits.
    PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
    PS50994. INTEGRASE. 1 hit.
    PS50879. RNASE_H. 1 hit.
    PS50878. RT_POL. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q9TTC1-1 [UniParc]FASTAAdd to Basket

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    MGKMGSKRTV VAGATGSKVY PWTTKRLLKI GQKQVTHSFL VIPECPAPLL     50
    GRDLLTKLKA QIQFSTEGPQ VTWEDRPAMC LVLNLEEEYR LHEKPVPPSI 100
    DPSWLQLFPM VWAEKAGMGL ANQVPPVVVE LKSDASPVAV RQYPMSKEAR 150
    EGIRPHIQRF LDLGILVPCQ SPWNTPLLPV KKPGTNDYRP VQDLREVNKR 200
    VQDIHPTVPN PYNLLSSLPP SHTWYSVLDL KDAFFCLKLH PNSQPLFAFE 250
    WRDPEKGNTG QLTWTRLPQG FKNSPTLFDE ALHRDLASFR ALNPQVVMLQ 300
    YVDDLLVAAP TYRDCKEGTR RLLQELSKLG YRVSAKKAQL CREEVTYLGY 350
    LLKGGKRWLT PARKATVMKI PTPTTPRQVR EFLGTAGFCR LWIPGFASLA 400
    APLYPLTREK VPFTWTEAHQ EAFGRIKEAL LSAPALALPD LTKPFALYVD 450
    EKEGVARGVL TQTLGPWRRP VAYLSKKLDP VASGWPTCLK AIAAVALLLK 500
    DADKLTLGQN VLVIAPHNLE SIVRQPPDRW MTNARMTHYQ SLLLNERVSF 550
    APPAILNPAT LLPVESDDTP IHICSEILAE ETGTRPDLRD QPLPGVPAWY 600
    TDGSSFIMDG RRQAGAAIVD NKRTVWASNL PEGTSAQKAE LIALTQALRL 650
    AEGKSINIYT DSRYAFATAH VHGAIYKQRG LLTSAGKDIK NKEEILALLE 700
    AIHLPKRVAI IHCPGHQRGT DPVATGNRKA DEAAKQAAQS TRILTETTKN 750
    QEHFEPTRGK IKPRELTPDQ GREFIQRLHQ LTHLGPDKLL QLVGRTSFHI 800
    PNLQSVVREI TSKCQVCAVT NAVTTYREPG RRQRGDRPGV YWEVDFTEVK 850
    PGRYGNRYLL VFIDTFSGWV EAFPTKTETA LTVCKKILEE ILPRFGIPKV 900
    LGSDNGPAFV AQVSQGLATQ LGIDWKLHCA YRPQSSGQVE RMNRTIKETL 950
    TKLALETGGK DWVTLLPLAL LRARNTPGQF GLTPYEILHG GPPPVLASGE 1000
    VVGSNGDFFP VLFTHLKALE VVRTQIWDQI KEAYRPGTVA IPHPFQVGDR 1050
    VLVRRHRSGS LEPRWKGPYL VLLTTPTAVK VDGIAAWVHA SHLKPAPPGA 1100
    PDESWELEKT DHPLKLRVRR RRNESTA 1127
    Length:1,127
    Mass (Da):125,817
    Last modified:May 1, 2000 - v1
    Checksum:i010ADD971CA957BF
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF151794 Genomic DNA. Translation: AAF15098.1.

    Keywords - Coding sequence diversityi

    RNA suppression of termination

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF151794 Genomic DNA. Translation: AAF15098.1 .

    3D structure databases

    ProteinModelPortali Q9TTC1.
    SMRi Q9TTC1. Positions 103-552, 583-738.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi A02.020.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 3.30.420.10. 2 hits.
    InterProi IPR001584. Integrase_cat-core.
    IPR018061. Pept_A2A_retrovirus_sg.
    IPR001995. Peptidase_A2_cat.
    IPR021109. Peptidase_aspartic_dom.
    IPR012337. RNaseH-like_dom.
    IPR002156. RNaseH_domain.
    IPR000477. RT_dom.
    [Graphical view ]
    Pfami PF00075. RNase_H. 1 hit.
    PF00665. rve. 1 hit.
    PF00077. RVP. 1 hit.
    PF00078. RVT_1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50630. SSF50630. 1 hit.
    SSF53098. SSF53098. 2 hits.
    PROSITEi PS50175. ASP_PROT_RETROV. 1 hit.
    PS50994. INTEGRASE. 1 hit.
    PS50879. RNASE_H. 1 hit.
    PS50878. RT_POL. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: a novel type C endogenous virus related to Gibbon ape leukemia virus."
      Hanger J.J., Bromham L.D., McKee J.J., O'Brien T.M., Robinson W.F.
      J. Virol. 74:4264-4272(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

    Entry informationi

    Entry nameiPOL_KORV
    AccessioniPrimary (citable) accession number: Q9TTC1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 5, 2006
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 78 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    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.
    Koala retrovirus is both a circulating virus and an endogenous retrovirus of koala, except in some isolated populations in south Australia.

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3