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P27408

- POLG_FCVF4

UniProt

P27408 - POLG_FCVF4

Protein

Genome polyprotein

Gene

ORF1

Organism
Feline calicivirus (strain Japanese F4) (FCV)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 82 (01 Oct 2014)
      Sequence version 2 (01 Jul 2008)
      Previous versions | rss
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    Functioni

    NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity By similarity.By similarity
    Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation By similarity.By similarity
    Protease-polymerase p76 processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved. Cleaves host translation initiation factor eIF4G1, eIF4G2 and PABP1 thereby inducing a shutdown of host protein synthesis. This shutdown may not prevent viral mRNA from being translated since viral Vpg replaces the cap. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation. It is also an RNA-directed RNA polymerase which replicates genomic and antigenomic viral RNA by recognizing specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs By similarity.By similarity

    Catalytic activityi

    NTP + H2O = NDP + phosphate.
    Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|-Xaa and the P1' position is occupied by Gly-|-Yaa.
    Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei46 – 472Cleavage; by Pro-PolBy similarity
    Sitei331 – 3322Cleavage; by Pro-PolBy similarity
    Sitei685 – 6862Cleavage; by Pro-PolBy similarity
    Sitei960 – 9612Cleavage; by Pro-PolBy similarity
    Sitei1071 – 10722Cleavage; by Pro-PolBy similarity
    Active sitei1110 – 11101For protease activity1 Publication
    Active sitei1131 – 11311For protease activity1 Publication
    Active sitei1193 – 11931For protease activity1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi484 – 4918ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. cysteine-type endopeptidase activity Source: InterPro
    3. RNA binding Source: InterPro
    4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
    5. RNA helicase activity Source: InterPro

    GO - Biological processi

    1. RNA-protein covalent cross-linking Source: UniProtKB-KW
    2. suppression by virus of host gene expression Source: UniProtKB-KW
    3. transcription, DNA-templated Source: InterPro
    4. viral RNA genome replication Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

    Keywords - Biological processi

    Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Viral RNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Protein family/group databases

    MEROPSiC24.002.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Genome polyprotein
    Cleaved into the following 6 chains:
    Alternative name(s):
    p39
    Alternative name(s):
    VPg
    p13
    Protease-polymerase p76 (EC:2.7.7.48, EC:3.4.22.66)
    Short name:
    Pro-Pol
    Gene namesi
    ORF Names:ORF1
    OrganismiFeline calicivirus (strain Japanese F4) (FCV)
    Taxonomic identifieri11980 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
    Virus hostiFelidae (cat family) [TaxID: 9681]
    ProteomesiUP000008668: Genome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi1079 – 10791H → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1093 – 10931H → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1099 – 10991H → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1102 – 11021H → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1110 – 11101H → A: Complete loss of protease activity in vitro. 1 Publication
    Mutagenesisi1121 – 11211E → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1125 – 11251D → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1131 – 11311E → A: Complete loss of protease activity in vitro. 1 Publication
    Mutagenesisi1155 – 11551D → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1164 – 11641E → A: No effect on protease activity in vitro. 1 Publication
    Mutagenesisi1193 – 11931C → A: Complete loss of protease activity in vitro. 1 Publication
    Mutagenesisi1208 – 12081H → A: Complete loss of protease activity in vitro. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 17631763Genome polyproteinPRO_0000341991Add
    BLAST
    Chaini1 – 4646Protein p5.6PRO_0000341992Add
    BLAST
    Chaini47 – 331285Protein p32PRO_0000341993Add
    BLAST
    Chaini332 – 685354NTPasePRO_0000341994Add
    BLAST
    Chaini686 – 960275Protein p30PRO_0000341995Add
    BLAST
    Chaini961 – 1071111Viral genome-linked proteinPRO_0000341996Add
    BLAST
    Chaini1072 – 1763692Protease-polymerase p76PRO_0000036899Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei984 – 9841O-(5'-phospho-RNA)-tyrosineBy similarity

    Post-translational modificationi

    Specific enzymatic cleavages in vivo yield mature proteins. Pro-Pol is first autocatalytically cleaved, then processes the whole polyprotein.
    VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity.By similarity

    Keywords - PTMi

    Covalent protein-RNA linkage, Phosphoprotein

    Interactioni

    Subunit structurei

    Protein p32: homodimer, interacts with NTPase, protein p30 and Pro-Pol. Viral genome-linked protein interacts with capsid protein and Pro-Pol. Protease-polymerase p76: Homooligomers, interacts with Vpg, protein p32 and may interact with capsid protein By similarity.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliP27408.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini458 – 614157SF3 helicasePROSITE-ProRule annotationAdd
    BLAST
    Domaini1095 – 1199105Peptidase C24Add
    BLAST
    Domaini1478 – 1603126RdRp catalyticPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    Protease-polymerase is composed of two domains displaying two different catalytic activity. These activities may act independently By similarity.By similarity

    Sequence similaritiesi

    Contains 1 peptidase C24 domain.Curated
    Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
    Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di3.40.50.300. 4 hits.
    InterProiIPR003593. AAA+_ATPase.
    IPR004004. Helic/Pol/Pept_Calicivir-typ.
    IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR014759. Helicase_SF3_ssRNA_vir.
    IPR027417. P-loop_NTPase.
    IPR000317. Peptidase_C24.
    IPR001205. RNA-dir_pol_C.
    IPR007094. RNA-dir_pol_PSvirus.
    IPR009003. Trypsin-like_Pept_dom.
    [Graphical view]
    PfamiPF03510. Peptidase_C24. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view]
    PRINTSiPR00916. 2CENDOPTASE.
    PR00918. CALICVIRUSNS.
    SMARTiSM00382. AAA. 1 hit.
    [Graphical view]
    SUPFAMiSSF50494. SSF50494. 1 hit.
    SSF52540. SSF52540. 4 hits.
    PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P27408-1 [UniParc]FASTAAdd to Basket

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    MSQTLSFVLK THSVRKDFVH SVKVTLARRR DLQYLYNKLA RTMRAEACPS     50
    CSSYDVCPNC TSSDIPDNGS STTSIPSWED VTKTSTYSLL LSEDTSDELC 100
    PDDLVNVAAH IRKALSTQAH PANTEMCKEQ LTSLLVMAEA MLPQRSRASI 150
    PLHQQHQAAR LEWREKFFSK PLDFLLERIG VSKDILQITA IWKIILEKAC 200
    YCKSYGEQWF CAAKQKLREM RTFESDTLKP LVGAFIDGLR FMTVDNPNPM 250
    GFLPKLIGLV KPLNLAMIID NHENTLSGWV VTLTAIMELY NITECTIDVI 300
    TSLVTGFYDK ISKATKFFSQ VKALFTGFRS EDVANSFWYM AAAILCYLIT 350
    GLIPNNGRFS KIKACLSGAT TLVSGIIATQ KLAAMFATWN SESIVNELSA 400
    RTVAISELNN PTTTSDTDSV ERLLELAKIL HEEIKVHTLN PIMQSYNPIL 450
    RNLMSTLDGV ITSCNKRKAI ARKRQVPVCY ILTGPPGCGK TTAAQALAKK 500
    LSDQEPSVIN LDVDHHDTYT GNEVCIIDEF DSSDKVDYAN FVIGMVNSAP 550
    MVLNCDMLEN KGKLFTSKYI IMTSNSETPV KPSSKRAGAF YRRVTIIDVT 600
    NPLVESHKRA RPGTSVPRSC YKKNFSHLSL AKRGAECWCK EYVLDPKGLQ 650
    HQTIKAPPPT FLNIDSLAQT MKQDFVLKNM AFEAEDGCSE HRYGFICQQS 700
    EVETVRRLLN AIRARLNATF TVCVGPEASH SIGCTAHVLT PDEPFNGRRF 750
    IVSRCNEASL AALEGNCVQS ALGVCMSNKD LTHLCHFIRG KIVNDSVRLD 800
    ELPANQHVVT VNSVFDLAWA LRRHLTLTGQ FQAIRAAYDV LTVPDKVPAM 850
    LRHWMDETSF SDEHVVTQFV TPGGVVILES CGGARIWALG HNVIRAGGVT 900
    ATPTGGCVRL VGLSAQTLPW SEIFRELFTL LGRIWSSIKV STLVLTALGM 950
    YASRFRPKSE AKGKTKSKIG PYRGRGVALT DDEYDEWREH NANRKLDLSV 1000
    EDFLMLRHRA ALGADDADAV KFRSWWNSRT RPGDGFEDVT VIGKGGVKHE 1050
    KIRTSTLRAV DRGYDVSFAE ESGPGTKFHK NAIGSVTDVC GEHKGYCVHM 1100
    GHGVYASVAH VVKGDSYFLG ERIFDVKTNG EFCCFRSTKI LPSAAPFFSG 1150
    KPTRDPWGSP VATEWKPKAY TTTSGKIVGC FATTSTETHP GDCGLPYIDD 1200
    NGRVTGLHTG SGGPKTPSAK LVVPYIHIDM KNKSVTPQKY DETKPNISYK 1250
    GLVCKQLDEI RIIPKGTRLH VSPAHVDDFE ECSHQPASLG SGDPRCPKSL 1300
    TAIVVDSLKP YCDRVEGPPH DVLHRVQKML IDHLSGFVPM NISSETSMLS 1350
    AFHKLNHDTS CGPYLGGRKK DHMVNGEPDK QLLDLLSSKW KLATQGIALP 1400
    HEYTIGLKDE LRPIEKVQEG KRRMIWGCDV GVATVCAAAF KGVSDAITAN 1450
    HQYGPIQVGI NMDSPSVEVL YQRIKSAAKV FAVDYSKWDS TQSPRVSAAS 1500
    IDILRYFSDR SPIVDSAANT LKSPPIAIFN GVAVKVASGL PSGMPLTSVI 1550
    NSLNHCMYVG CAILQSLEAR QIPVTWNLFS SFDMMTYGDD GVYMFPTMFA 1600
    SVSDQIFGNL SAYGLKPTRV DKSVGAIESI DPESVVFLKR TITRTPNGIR 1650
    GLLDRSSIIR QFFYIKGENS DDWKTPPKTI DPTSRGQQLW NACLYASQHG 1700
    VEFYNKVLKL AMRAVEYEGL HLKPPSYSSA LEHYNSQFNG VEARSDQINM 1750
    SDVTALHCDV FEV 1763
    Length:1,763
    Mass (Da):194,988
    Last modified:July 1, 2008 - v2
    Checksum:i173626D6C862E46C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti1417 – 14171V → M in BAA14370. (PubMed:1853578)Curated
    Sequence conflicti1485 – 14873YSK → FSN in BAA14370. (PubMed:1853578)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D31836 Genomic RNA. Translation: BAA06622.2.
    D90357 Genomic RNA. Translation: BAA14370.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D31836 Genomic RNA. Translation: BAA06622.2 .
    D90357 Genomic RNA. Translation: BAA14370.1 .

    3D structure databases

    ProteinModelPortali P27408.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi C24.002.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 3.40.50.300. 4 hits.
    InterProi IPR003593. AAA+_ATPase.
    IPR004004. Helic/Pol/Pept_Calicivir-typ.
    IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR014759. Helicase_SF3_ssRNA_vir.
    IPR027417. P-loop_NTPase.
    IPR000317. Peptidase_C24.
    IPR001205. RNA-dir_pol_C.
    IPR007094. RNA-dir_pol_PSvirus.
    IPR009003. Trypsin-like_Pept_dom.
    [Graphical view ]
    Pfami PF03510. Peptidase_C24. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view ]
    PRINTSi PR00916. 2CENDOPTASE.
    PR00918. CALICVIRUSNS.
    SMARTi SM00382. AAA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50494. SSF50494. 1 hit.
    SSF52540. SSF52540. 4 hits.
    PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The molecular cloning and sequence of an open reading frame encoding for non-structural proteins of feline calicivirus F4 strain isolated in Japan."
      Oshikamo R., Tohya Y., Kawaguchi Y., Tomonaga K., Maeda K., Takeda N., Utagawa E., Kai C., Mikami T.
      J. Vet. Med. Sci. 56:1093-1099(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1383-1763.
    3. "Highly conserved configuration of catalytic amino acid residues among calicivirus-encoded proteases."
      Oka T., Yamamoto M., Yokoyama M., Ogawa S., Hansman G.S., Katayama K., Miyashita K., Takagi H., Tohya Y., Sato H., Takeda N.
      J. Virol. 81:6798-6806(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITES, MUTAGENESIS OF HIS-1079; HIS-1093; HIS-1099; HIS-1102; HIS-1110; GLU-1121; ASP-1125; GLU-1131; ASP-1155; GLU-1164; CYS-1193 AND HIS-1208.

    Entry informationi

    Entry nameiPOLG_FCVF4
    AccessioniPrimary (citable) accession number: P27408
    Secondary accession number(s): Q66913
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: July 1, 2008
    Last modified: October 1, 2014
    This is version 82 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome

    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