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Q86117

- POLG_RHDVS

UniProt

Q86117 - POLG_RHDVS

Protein

Genome polyprotein

Gene

ORF1

Organism
Rabbit hemorrhagic disease virus (strain SD) (Ra/LV/RHDV/SD/1989/FR) (RHDV-SD)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 84 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    NTPase presumably plays a role in replication.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
    3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved.By similarity
    RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications 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.PROSITE-ProRule annotation
    Capsid protein VP60 self assembles to form an icosahedral capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate VP2 proteins and genomic or subgenomic RNA. Attaches virion to target cells by binding histo-blood group antigens, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm 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
    Sitei143 – 1442Cleavage; by 3CLproBy similarity
    Sitei339 – 3402Cleavage; by 3CLproBy similarity
    Sitei718 – 7192Cleavage; by 3CLproBy similarity
    Sitei936 – 9372Cleavage; by hostBy similarity
    Sitei993 – 9942Cleavage; by 3CLproBy similarity
    Sitei1108 – 11092Cleavage; by 3CLproBy similarity
    Active sitei1135 – 11351For 3CLpro activityBy similarity
    Active sitei1159 – 11591For 3CLpro activityBy similarity
    Active sitei1212 – 12121For 3CLpro activitySequence Analysis
    Sitei1251 – 12522Cleavage; by 3CLproBy similarity
    Sitei1767 – 17682Cleavage; by 3CLproBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi522 – 5298ATPPROSITE-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. transcription, DNA-templated Source: InterPro
    3. viral RNA genome replication Source: InterPro

    Keywords - Molecular functioni

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

    Keywords - Biological processi

    Viral RNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Protein family/group databases

    MEROPSiC24.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Genome polyprotein
    Alternative name(s):
    p254
    Cleaved into the following 11 chains:
    Alternative name(s):
    2C-like protein
    P2C
    p37
    Alternative name(s):
    VPg
    p13
    3C-like protease (EC:3.4.22.66)
    Short name:
    3CLpro
    Alternative name(s):
    Calicivirin
    Thiol protease P3C
    p15
    Alternative name(s):
    3Dpol
    p58
    Gene namesi
    ORF Names:ORF1
    OrganismiRabbit hemorrhagic disease virus (strain SD) (Ra/LV/RHDV/SD/1989/FR) (RHDV-SD)
    Taxonomic identifieri314535 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeLagovirus
    Virus hostiOryctolagus cuniculus (Rabbit) [TaxID: 9986]

    Subcellular locationi

    GO - Cellular componenti

    1. host cell cytoplasm Source: UniProtKB-SubCell
    2. viral capsid Source: UniProtKB-KW

    Keywords - Cellular componenti

    Capsid protein, Host cytoplasm, Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 23442344Genome polyproteinPRO_0000342007Add
    BLAST
    Chaini1 – 143143Protein p16By similarityPRO_0000036968Add
    BLAST
    Chaini144 – 339196Protein p23By similarityPRO_0000036969Add
    BLAST
    Chaini340 – 718379NTPaseBy similarityPRO_0000036970Add
    BLAST
    Chaini712 – 1108397Precursor p41By similarityPRO_0000342008Add
    BLAST
    Chaini712 – 936225Protein p23/2By similarityPRO_0000342009Add
    BLAST
    Chaini719 – 993275Protein p29By similarityPRO_0000036971Add
    BLAST
    Chaini937 – 1108172Protein p18By similarityPRO_0000342010Add
    BLAST
    Chaini994 – 1108115Viral genome-linked proteinBy similarityPRO_0000036972Add
    BLAST
    Chaini1109 – 12511433C-like proteaseBy similarityPRO_0000036973Add
    BLAST
    Chaini1252 – 1767516RNA-directed RNA polymeraseBy similarityPRO_0000036974Add
    BLAST
    Chaini1768 – 2344577Capsid protein VP60By similarityPRO_0000036976Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1014 – 10141O-(5'-phospho-RNA)-tyrosineBy similarity
    Disulfide bondi1584 ↔ 1591By similarity

    Post-translational modificationi

    Specific enzymatic cleavages by its own cysteine protease yield mature proteins. The protease cleaves itself from the nascent polyprotein autocatalytically. Precursor p41 can be cleaved by viral 3CLpro into protein p19 and VPg, or cleaved by host protease into protein p23/2 and protein p18 By similarity.By similarity
    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, Disulfide bond, Phosphoprotein

    Interactioni

    Subunit structurei

    Binds to histo-blood group antigens at surface of target cells.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ86117.
    SMRiQ86117. Positions 1256-1752.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini492 – 653162SF3 helicasePROSITE-ProRule annotationAdd
    BLAST
    Domaini1120 – 121899Peptidase C24Add
    BLAST
    Domaini1495 – 1619125RdRp catalyticPROSITE-ProRule annotationAdd
    BLAST

    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

    Gene3Di2.60.120.20. 1 hit.
    3.40.50.300. 2 hits.
    InterProiIPR003593. AAA+_ATPase.
    IPR004005. Calicivirus_coat.
    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.
    IPR029053. Viral_coat.
    [Graphical view]
    PfamiPF00915. Calici_coat. 1 hit.
    PF03510. 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. 1 hit.
    PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 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 alternative promoter usage. Align

    Isoform Genome polyprotein (identifier: Q86117-1) [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

    MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFLGQ     50
    YGKEGPLETC NKCGKWLNGF GCFGLEDLGD VCLCSIAQQK HKFGPVCLCN 100
    RAYIHDCGRW RRRSRFLKHY KALNKVIPCA YQFDESFSTP VFEGEVDDLF 150
    VELGAPTSMG FMDKKLLKKG KKLMDKFVDV DEPCLTSRDA SLLDSIASDN 200
    TIRAKWEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV TWYTKLGNIT 250
    EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV 300
    NLLAILMDWT NDLTGFVTTL VRLLELYGVV QATVNLIVEG VKSFWDKVVC 350
    ATDRCFDLLK RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT 400
    TFMKGAGKLT TFAGVIGAIR TLWITINQHM VAKDLTSIQQ KVMTVVKMAN 450
    EAATLDQLEI VSCLCSDLEN TLTNRCTLPS YNQHLGILNA SQKVISDLHT 500
    MVLGKINMTK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG CQHPSTINFG 550
    LDHFDSYTGE EVAIADEFNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK 600
    NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR 650
    HGSKPGRSCY SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY 700
    SELLDLIKSE HPDVASFEGA NRFNFVYPDA QYDQALLMWK QYFVMYGCVA 750
    RLAKNFVDDI PYNQVHISRA SDPKIEGCVE YQCKFQHLWR MVPQFVLGCV 800
    NMTNQLGTPL TQQQLDRVTN GVEGVTVTTV NNILPFHSQT TLINPSFIKL 850
    IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDDPV 900
    STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL 950
    ISGFSWRQIA HLFVEVISRL CANHLVNLAT MAALGAVATK AFQGVKGKTK 1000
    RGRGARVNLG NDEYDEWQAA RREFVNAHDM TAEEYLAMKN KAAMGSDDQD 1050
    SVMFRSWWTR RQLRPDEDQV TIVGRGGVRN EVIRTRVRQT PKGPKTLDDG 1100
    GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS CSEVVTCSPT 1150
    TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA 1200
    YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY 1250
    ETSNFFCGEP IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPEEYKTGYR 1300
    PANLGRSDPD SDKSLMNIAV KNLQVYQQEP KLDKVDEFIE RAAADVLGYL 1350
    RFLTKGERQV NLNFKAAFNT LDLSTSCGPF VPGKKIDHVK DGVMDQVLAK 1400
    HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL LWGCDVGVAV 1450
    CAAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL 1500
    DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI 1550
    VQTKRGLPSG MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF 1600
    YTYGDDGVYA MTPMMVSLLP AIIENLRDYG LLPTAADKTE FIDVCPLNKI 1650
    SFLKRTFELT DIGWISKLDK SSILRQLEWS KTTSRHMMIE ETYDLAKEER 1700
    GVQLEELQVA AAAHGQEFFN FVRKELERQQ AYTQFSVYSY DAARKILADR 1750
    KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGMDPGVV 1800
    ATTSVVTAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA 1850
    PGSILYTVQH SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVA 1900
    AVIPPGIEIG PGLEVRQFPH VVIDARSLEP VTITMPDLRP NMYHPTGDPG 1950
    LVPTLVLSVY NNLINPFGGS TSAIQVTVET RPSEDFEFVM IRAPSSKTVD 2000
    SISPAGLLTT PVLTGVGNDN RWNGQIVGLQ PVPGGFSTCN RHWNLNGSTY 2050
    GWSSPRFADI DHRRGSASYP GNNATNVLQF WYANAGSAID NPISQVAPDG 2100
    FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP 2150
    GNLQPTTNTS GSQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPSANAIT 2200
    YTPQPDRIVT TPGTPAAAPV GKNTPIMFAS VVRRTGDVNA TAGSANGTQY 2250
    GRGSQPLPVT IGLSLNNYSS ALMPGQFFVW QLTFASGFME IGLSVDGYFY 2300
    AGTGASTTLI DLIELIDVRP VGPRPSKSTL VFNLGGTANG FSYV 2344

    Note: Produced from the genomic RNA.

    Length:2,344
    Mass (Da):257,122
    Last modified:November 1, 1996 - v1
    Checksum:i193B1D447658FB77
    GO
    Isoform Subgenomic capsid protein VP60 (identifier: Q86117-2) [UniParc]FASTAAdd to Basket

    Also known as: VP1

    The sequence of this isoform differs from the canonical sequence as follows:
         1-1765: Missing.

    Note: Produced from the subgenomic RNA.

    Show »
    Length:579
    Mass (Da):60,309
    Checksum:i8A0F6C17C1B17DD0
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 17651765Missing in isoform Subgenomic capsid protein VP60. CuratedVSP_034382Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z29514 Genomic RNA. Translation: CAA82635.1.

    Keywords - Coding sequence diversityi

    Alternative promoter usage

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z29514 Genomic RNA. Translation: CAA82635.1 .

    3D structure databases

    ProteinModelPortali Q86117.
    SMRi Q86117. Positions 1256-1752.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi C24.001.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 2.60.120.20. 1 hit.
    3.40.50.300. 2 hits.
    InterProi IPR003593. AAA+_ATPase.
    IPR004005. Calicivirus_coat.
    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.
    IPR029053. Viral_coat.
    [Graphical view ]
    Pfami PF00915. Calici_coat. 1 hit.
    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. 1 hit.
    PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and genomic organization of a rabbit haemorrhagic disease virus isolate from a wild rabbit."
      Rasschaert D., Huguet S., Madelaine M.-F., Vautherot J.-F.
      Virus Genes 9:121-132(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

    Entry informationi

    Entry nameiPOLG_RHDVS
    AccessioniPrimary (citable) accession number: Q86117
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 84 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Two differents RNAs lead the expression of the capsid protein. One arises from the cleavage of the polyprotein translated from the genomic RNA and the other from the translation of a subgenomic RNA derived from the (-)RNA template. Capsid protein expressed from the subgenomic mRNA is produced in much larger amounts than the cleaved one By similarity.By similarity

    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