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P27411

- POLG_RHDV3

UniProt

P27411 - POLG_RHDV3

Protein

Genome polyprotein

Gene

ORF1

Organism
Rabbit hemorrhagic disease virus (strain V-351) (Ra/LV/RHDV/V351/1991/CK) (RHDV-V351)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 87 (01 Oct 2014)
      Sequence version 2 (29 Mar 2005)
      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

    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 V-351) (Ra/LV/RHDV/V351/1991/CK) (RHDV-V351)
    Taxonomic identifieri11977 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeLagovirus
    Virus hostiOryctolagus cuniculus (Rabbit) [TaxID: 9986]
    ProteomesiUP000008652: Genome

    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_0000342011Add
    BLAST
    Chaini1 – 143143Protein p16By similarityPRO_0000036977Add
    BLAST
    Chaini144 – 339196Protein p23By similarityPRO_0000036978Add
    BLAST
    Chaini340 – 718379NTPaseBy similarityPRO_0000036979Add
    BLAST
    Chaini712 – 1108397Precursor p41By similarityPRO_0000342012Add
    BLAST
    Chaini712 – 936225Protein p23/2By similarityPRO_0000342013Add
    BLAST
    Chaini719 – 993275Protein p29By similarityPRO_0000036980Add
    BLAST
    Chaini937 – 1108172Protein p18PRO_0000342014Add
    BLAST
    Chaini994 – 1108115Viral genome-linked proteinBy similarityPRO_0000036981Add
    BLAST
    Chaini1109 – 12511433C-like proteaseBy similarityPRO_0000036982Add
    BLAST
    Chaini1252 – 1767516RNA-directed RNA polymeraseBy similarityPRO_0000036983Add
    BLAST
    Chaini1768 – 2344577Capsid protein VP60By similarityPRO_0000036985Add
    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

    ProteinModelPortaliP27411.
    SMRiP27411. 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: P27411-1) [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 LSFFLDLRDK TPPCCIRATG RLAWPVFPGQ     50
    NGKEGPLETC NMCGKWLNGF GNFGLEDLGD VCLRSIAQQK HKFGPVCLCN 100
    RVYLHDCGRW RRRSRFLKHY KALNKVIPCA YQFVESFPTP IFEGEVDDLF 150
    VELGAPTSMG FMDKKLLKKG KKLMDKFVDV DEPCLTSRDA SLLDSIASDN 200
    TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNWPANPV TWYRKLGNIT 250
    KKGKQWAKKV VYGARKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFNPV 300
    NLLAILMDWN NDLTGFFATL VRLLELYGVV QATVNLIIEG VKSFWDKVVC 350
    ATDRCFDLLK RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT 400
    TFMKGAGKLT TFAGVVGAIR TLWITINQHM VAKDLTSVQQ KVMTVVKMAN 450
    EAATLDQLEI VSCLCSDLET TLTNRCTLPS YNQHLGILNA SQKVISDLHT 500
    MVLGKINTSK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG CQHPSTINFG 550
    LDHFDSYTGE EVAIADESNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK 600
    NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR 650
    HGSKPGKSCY NKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVTPREYKY 700
    SELLDLIKSE HPDVASFEGA NKFNFVYPDA QYDQALLMWK QYFVMYGCVA 750
    RLAKNFVDDI PYNQVHISRA SDPKIEGCVE YQCKFQHLWR MVPQFVLGCV 800
    NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILPFHSQT TLINPSFIKL 850
    IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGTLVRTLT GAATFSDDPV 900
    STTIICSNCT IQLHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL 950
    ISGFSWRQIA HLFVEVISHL CANHLVNLAT MAALGAVATK AFQGVKGKTK 1000
    RGRGARVNLG NDEYDEWQAA RREFVNAHDM TAEEYLAMKN KAAMGSDDQD 1050
    SIMFRSWWTR RQLRPDEDQV TIVGRSGVRN EVIRTRVRQT PRGPKTLDDG 1100
    GFYDNDYEGL PGFMRHNGSG RMIHIGNGLY ISNTHTARSS CSEIVTCSPT 1150
    TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA 1200
    YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY 1250
    ETSNFFCGEP IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPDEYKTGYR 1300
    PANLGRSDPD SDKSLMNIAV KNLQVYQQEP KLDKVDEFIE RAAADVLGYL 1350
    RFLTKGERQA NLNFKAAFNT LDLSTSCGPF APGKKIDHVK DGVMDQVLAK 1400
    HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL LWGCDVGVAV 1450
    CAAAVFHNIC YELKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL 1500
    DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI 1550
    VQTKRGLPSG MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF 1600
    YTYGDDGVYA MTPMMVSLLP AIIENLRDYG LSPTAADKTE FIDVCPLNKI 1650
    SFLKRTFELT DIGWVSKLDK SSILRQLEWS KTTSRHMVIE ETYDLAKEER 1700
    GVQLEELQVA AAAHGQEFFN FVCGELVRQQ AYTQFSVYSY DAARKILADR 1750
    KRVVSVVPDD EFVNVMEGKA RAAPQGEAAR TATTASVPGT TTDGMDPGVV 1800
    ATTSVITAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA 1850
    PGSILYTVQH SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVR 1900
    AVIPPGIEIG PGLEVRQFPH VVIDARSLEP VTITMPDLRP NMYHPTGDPG 1950
    LVPTLVLSVY NNLINPFGGS TSAIQVTVET RPSEDFEFVM IRAPSSKTVD 2000
    SISPAGLLTT PDLTGVGNDN RWNGQIVGLQ PVPGGFSTCN RHWNLNGSTY 2050
    GWSSPRFADI DHRKGSASYP GSNATNVLQF WYANAGSAID NPISQVAPDG 2100
    LPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP 2150
    GNLQPTTNTS GAQTVAKSIY AVVTGTAQNP AGLFVMASGI ISTPNASAIT 2200
    YTPQPDRIVT TPGTPAAAPV GKNTPIMFAS VVRRTGDVNA TAGSANGTQY 2250
    GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW QLTFASGFME IGLSVDGYFY 2300
    AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG FSYV 2344

    Note: Produced from the genomic RNA.

    Length:2,344
    Mass (Da):256,908
    Last modified:March 29, 2005 - v2
    Checksum:i12FB095E76F65410
    GO
    Isoform Subgenomic capsid protein VP60 (identifier: P27411-2) [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):60,335
    Checksum:i74A2F7DCCEB456F8
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti2245 – 22451A → V in CAA77633. (PubMed:1497750)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 17651765Missing in isoform Subgenomic capsid protein VP60. CuratedVSP_034383Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U54983 Genomic RNA. Translation: AAB02225.1.
    Z11535 Genomic RNA. Translation: CAA77633.1.
    PIRiS22134.

    Keywords - Coding sequence diversityi

    Alternative promoter usage

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U54983 Genomic RNA. Translation: AAB02225.1 .
    Z11535 Genomic RNA. Translation: CAA77633.1 .
    PIRi S22134.

    3D structure databases

    ProteinModelPortali P27411.
    SMRi P27411. Positions 1256-1752.
    ModBasei Search...
    MobiDBi Search...

    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. "The complete nucleotide sequence of rabbit haemorrhagic disease virus (Czech strain V351): use of the polymerase chain reaction to detect replication in Australian vertebrates and analysis of viral population sequence variation."
      Gould A.R., Kattenbelt J.A., Lenghaus C., Morrissy C., Chamberlain T., Collins B.J., Westbury H.A.
      Virus Res. 47:7-17(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. "Genomic 3' terminal sequence comparison of three isolates of rabbit haemorrhagic disease virus."
      Milton I.D., Vlasak R., Nowotny N., Rodak L., Carter M.J.
      FEMS Microbiol. Lett. 72:37-42(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2111-2344.

    Entry informationi

    Entry nameiPOLG_RHDV3
    AccessioniPrimary (citable) accession number: P27411
    Secondary accession number(s): Q86114
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: March 29, 2005
    Last modified: October 1, 2014
    This is version 87 of the entry and version 2 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

    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