ID   POLG_RHDVS              Reviewed;        2344 AA.
AC   Q86117;
DT   29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   24-JAN-2024, entry version 119.
DE   RecName: Full=Genome polyprotein;
DE   AltName: Full=p254;
DE   Contains:
DE     RecName: Full=Protein p16;
DE   Contains:
DE     RecName: Full=Protein p23;
DE   Contains:
DE     RecName: Full=NTPase;
DE              EC=3.6.1.15;
DE     AltName: Full=2C-like protein;
DE     AltName: Full=P2C;
DE     AltName: Full=p37;
DE   Contains:
DE     RecName: Full=Precursor p41;
DE   Contains:
DE     RecName: Full=Protein p29;
DE   Contains:
DE     RecName: Full=Protein p23/2;
DE   Contains:
DE     RecName: Full=Protein p18;
DE   Contains:
DE     RecName: Full=Viral genome-linked protein;
DE     AltName: Full=VPg;
DE     AltName: Full=p13;
DE   Contains:
DE     RecName: Full=3C-like protease;
DE              Short=3CLpro;
DE              EC=3.4.22.66;
DE     AltName: Full=Calicivirin;
DE     AltName: Full=Thiol protease P3C;
DE     AltName: Full=p15;
DE   Contains:
DE     RecName: Full=RNA-directed RNA polymerase;
DE              EC=2.7.7.48;
DE     AltName: Full=3Dpol;
DE     AltName: Full=p58;
DE   Contains:
DE     RecName: Full=Capsid protein VP60;
GN   ORFNames=ORF1;
OS   Rabbit hemorrhagic disease virus (strain SD) (Ra/LV/RHDV/SD/1989/FR)
OS   (RHDV-SD).
OC   Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC   Picornavirales; Caliciviridae; Lagovirus; Rabbit hemorrhagic disease virus.
OX   NCBI_TaxID=314535;
OH   NCBI_TaxID=9986; Oryctolagus cuniculus (Rabbit).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=7732658; DOI=10.1007/bf01702655;
RA   Rasschaert D., Huguet S., Madelaine M.-F., Vautherot J.-F.;
RT   "Sequence and genomic organization of a rabbit haemorrhagic disease virus
RT   isolate from a wild rabbit.";
RL   Virus Genes 9:121-132(1995).
CC   -!- FUNCTION: NTPase presumably plays a role in replication. {ECO:0000250}.
CC   -!- FUNCTION: Viral genome-linked protein is covalently linked to the 5'-
CC       end of the positive-strand, negative-strand genomic RNAs and subgenomic
CC       RNA. Acts as a genome-linked replication primer. May recruit ribosome
CC       to viral RNA thereby promoting viral proteins translation (By
CC       similarity). {ECO:0000250}.
CC   -!- FUNCTION: 3C-like protease processes the polyprotein: 3CLpro-RdRp (p72)
CC       is first released by autocleavage, then all other proteins are cleaved.
CC       {ECO:0000250}.
CC   -!- FUNCTION: RNA-directed RNA polymerase replicates genomic and
CC       antigenomic RNA by recognizing replications specific signals.
CC       Transcribes also a subgenomic mRNA by initiating RNA synthesis
CC       internally on antigenomic RNA. This sgRNA codes for structural
CC       proteins. Catalyzes the covalent attachment VPg with viral RNAs (By
CC       similarity). {ECO:0000255|PROSITE-ProRule:PRU00539}.
CC   -!- FUNCTION: Capsid protein VP60 self assembles to form an icosahedral
CC       capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of
CC       180 capsid proteins. A smaller form of capsid with a diameter of 23 nm
CC       might be capsid proteins assembled as icosahedron with T=1 symmetry.
CC       The capsid encapsulate VP2 proteins and genomic or subgenomic RNA.
CC       Attaches virion to target cells by binding histo-blood group antigens,
CC       inducing endocytosis of the viral particle. Acidification of the
CC       endosome induces conformational change of capsid protein thereby
CC       injecting virus genomic RNA into host cytoplasm (By similarity).
CC       {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-
CC         diphosphate + H(+) + phosphate; Xref=Rhea:RHEA:23680,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:57930, ChEBI:CHEBI:61557; EC=3.6.1.15;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC         RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC         COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC         EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endopeptidase with a preference for cleavage when the P1
CC         position is occupied by Glu-|-Xaa and the P1' position is occupied by
CC         Gly-|-Yaa.; EC=3.4.22.66; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU01242};
CC   -!- SUBUNIT: Binds to histo-blood group antigens at surface of target
CC       cells. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: [Capsid protein VP60]: Virion. Host cytoplasm
CC       {ECO:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative promoter usage; Named isoforms=2;
CC       Name=Genome polyprotein;
CC         IsoId=Q86117-1; Sequence=Displayed;
CC       Name=Subgenomic capsid protein VP60; Synonyms=VP1;
CC         IsoId=Q86117-2; Sequence=VSP_034382;
CC   -!- PTM: Specific enzymatic cleavages by its own cysteine protease yield
CC       mature proteins. The protease cleaves itself from the nascent
CC       polyprotein autocatalytically. Precursor p41 can be cleaved by viral
CC       3CLpro into protein p19 and VPg, or cleaved by host protease into
CC       protein p23/2 and protein p18 (By similarity). {ECO:0000250}.
CC   -!- PTM: VPg is uridylylated by the polymerase and is covalently attached
CC       to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This
CC       uridylylated form acts as a nucleotide-peptide primer for the
CC       polymerase (By similarity). {ECO:0000250}.
CC   -!- MISCELLANEOUS: Two different RNAs lead the expression of the capsid
CC       protein. One arises from the cleavage of the polyprotein translated
CC       from the genomic RNA and the other from the translation of a subgenomic
CC       RNA derived from the (-)RNA template. Capsid protein expressed from the
CC       subgenomic mRNA is produced in much larger amounts than the cleaved one
CC       (By similarity). {ECO:0000250}.
CC   -!- MISCELLANEOUS: [Isoform Genome polyprotein]: Produced from the genomic
CC       RNA.
CC   -!- MISCELLANEOUS: [Isoform Subgenomic capsid protein VP60]: Produced from
CC       the subgenomic RNA. {ECO:0000305}.
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DR   EMBL; Z29514; CAA82635.1; -; Genomic_RNA.
DR   SMR; Q86117; -.
DR   MEROPS; C24.001; -.
DR   Proteomes; UP000121187; Genome.
DR   GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0019028; C:viral capsid; IEA:UniProtKB-KW.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR   GO; GO:0017111; F:ribonucleoside triphosphate phosphatase activity; IEA:UniProtKB-EC.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:InterPro.
DR   GO; GO:0003968; F:RNA-dependent RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006351; P:DNA-templated transcription; IEA:InterPro.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR   CDD; cd00009; AAA; 1.
DR   CDD; cd23192; Caliciviridae_RdRp; 1.
DR   CDD; cd00205; rhv_like; 1.
DR   Gene3D; 1.10.260.110; -; 1.
DR   Gene3D; 1.20.960.20; -; 1.
DR   Gene3D; 2.60.120.20; -; 1.
DR   Gene3D; 3.30.70.270; -; 1.
DR   Gene3D; 4.10.8.20; DNA/RNA polymerases; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR   InterPro; IPR004005; Calicivirus_coat.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR004004; Helic/Pol/Pept_Calicivir-typ.
DR   InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
DR   InterPro; IPR014759; Helicase_SF3_ssRNA_vir.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR000317; Peptidase_C24.
DR   InterPro; IPR009003; Peptidase_S1_PA.
DR   InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR   InterPro; IPR033703; Rhv-like.
DR   InterPro; IPR001205; RNA-dir_pol_C.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   InterPro; IPR029053; Viral_coat.
DR   InterPro; IPR049434; VPg.
DR   Pfam; PF00915; Calici_coat; 1.
DR   Pfam; PF03510; Peptidase_C24; 1.
DR   Pfam; PF00680; RdRP_1; 1.
DR   Pfam; PF00910; RNA_helicase; 1.
DR   Pfam; PF20915; VPg; 1.
DR   PRINTS; PR00916; 2CENDOPTASE.
DR   PRINTS; PR00918; CALICVIRUSNS.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR   SUPFAM; SSF88633; Positive stranded ssRNA viruses; 1.
DR   SUPFAM; SSF50494; Trypsin-like serine proteases; 1.
DR   PROSITE; PS51894; CV_3CL_PRO; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
DR   PROSITE; PS51218; SF3_HELICASE_2; 1.
PE   3: Inferred from homology;
KW   Alternative promoter usage; ATP-binding; Capsid protein;
KW   Covalent protein-RNA linkage; Disulfide bond; Helicase; Host cytoplasm;
KW   Hydrolase; Nucleotide-binding; Nucleotidyltransferase; Phosphoprotein;
KW   Protease; RNA-directed RNA polymerase; Thiol protease; Transferase;
KW   Viral RNA replication; Virion.
FT   CHAIN           1..2344
FT                   /note="Genome polyprotein"
FT                   /id="PRO_0000342007"
FT   CHAIN           1..143
FT                   /note="Protein p16"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036968"
FT   CHAIN           144..339
FT                   /note="Protein p23"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036969"
FT   CHAIN           340..718
FT                   /note="NTPase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036970"
FT   CHAIN           712..1108
FT                   /note="Precursor p41"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000342008"
FT   CHAIN           712..936
FT                   /note="Protein p23/2"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000342009"
FT   CHAIN           719..993
FT                   /note="Protein p29"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036971"
FT   CHAIN           937..1108
FT                   /note="Protein p18"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000342010"
FT   CHAIN           994..1108
FT                   /note="Viral genome-linked protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036972"
FT   CHAIN           1109..1251
FT                   /note="3C-like protease"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036973"
FT   CHAIN           1252..1767
FT                   /note="RNA-directed RNA polymerase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036974"
FT   CHAIN           1768..2344
FT                   /note="Capsid protein VP60"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036976"
FT   DOMAIN          492..653
FT                   /note="SF3 helicase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT   DOMAIN          1109..1244
FT                   /note="Peptidase C24"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   DOMAIN          1495..1619
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          1771..1796
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1777..1791
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        1135
FT                   /note="For 3CLpro activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   ACT_SITE        1152
FT                   /note="For 3CLpro activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   ACT_SITE        1212
FT                   /note="For 3CLpro activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   BINDING         522..529
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT   SITE            143..144
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   SITE            339..340
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   SITE            718..719
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   SITE            936..937
FT                   /note="Cleavage; by host"
FT                   /evidence="ECO:0000250"
FT   SITE            993..994
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   SITE            1108..1109
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   SITE            1251..1252
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   SITE            1767..1768
FT                   /note="Cleavage; by 3CLpro"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         1014
FT                   /note="O-(5'-phospho-RNA)-tyrosine"
FT                   /evidence="ECO:0000250"
FT   DISULFID        1584..1591
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         1..1765
FT                   /note="Missing (in isoform Subgenomic capsid protein VP60)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_034382"
SQ   SEQUENCE   2344 AA;  257122 MW;  193B1D447658FB77 CRC64;
     MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFLGQ YGKEGPLETC
     NKCGKWLNGF GCFGLEDLGD VCLCSIAQQK HKFGPVCLCN RAYIHDCGRW RRRSRFLKHY
     KALNKVIPCA YQFDESFSTP VFEGEVDDLF VELGAPTSMG FMDKKLLKKG KKLMDKFVDV
     DEPCLTSRDA SLLDSIASDN TIRAKWEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV
     TWYTKLGNIT EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV
     NLLAILMDWT NDLTGFVTTL VRLLELYGVV QATVNLIVEG VKSFWDKVVC ATDRCFDLLK
     RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT TFMKGAGKLT TFAGVIGAIR
     TLWITINQHM VAKDLTSIQQ KVMTVVKMAN EAATLDQLEI VSCLCSDLEN TLTNRCTLPS
     YNQHLGILNA SQKVISDLHT MVLGKINMTK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG
     CQHPSTINFG LDHFDSYTGE EVAIADEFNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK
     NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR HGSKPGRSCY
     SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY SELLDLIKSE HPDVASFEGA
     NRFNFVYPDA QYDQALLMWK QYFVMYGCVA RLAKNFVDDI PYNQVHISRA SDPKIEGCVE
     YQCKFQHLWR MVPQFVLGCV NMTNQLGTPL TQQQLDRVTN GVEGVTVTTV NNILPFHSQT
     TLINPSFIKL IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDDPV
     STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL ISGFSWRQIA
     HLFVEVISRL CANHLVNLAT MAALGAVATK AFQGVKGKTK RGRGARVNLG NDEYDEWQAA
     RREFVNAHDM TAEEYLAMKN KAAMGSDDQD SVMFRSWWTR RQLRPDEDQV TIVGRGGVRN
     EVIRTRVRQT PKGPKTLDDG GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS
     CSEVVTCSPT TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA
     YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY ETSNFFCGEP
     IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPEEYKTGYR PANLGRSDPD SDKSLMNIAV
     KNLQVYQQEP KLDKVDEFIE RAAADVLGYL RFLTKGERQV NLNFKAAFNT LDLSTSCGPF
     VPGKKIDHVK DGVMDQVLAK HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL
     LWGCDVGVAV CAAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL
     DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI VQTKRGLPSG
     MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF YTYGDDGVYA MTPMMVSLLP
     AIIENLRDYG LLPTAADKTE FIDVCPLNKI SFLKRTFELT DIGWISKLDK SSILRQLEWS
     KTTSRHMMIE ETYDLAKEER GVQLEELQVA AAAHGQEFFN FVRKELERQQ AYTQFSVYSY
     DAARKILADR KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGMDPGVV
     ATTSVVTAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA PGSILYTVQH
     SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVA AVIPPGIEIG PGLEVRQFPH
     VVIDARSLEP VTITMPDLRP NMYHPTGDPG LVPTLVLSVY NNLINPFGGS TSAIQVTVET
     RPSEDFEFVM IRAPSSKTVD SISPAGLLTT PVLTGVGNDN RWNGQIVGLQ PVPGGFSTCN
     RHWNLNGSTY GWSSPRFADI DHRRGSASYP GNNATNVLQF WYANAGSAID NPISQVAPDG
     FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP GNLQPTTNTS
     GSQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPSANAIT YTPQPDRIVT TPGTPAAAPV
     GKNTPIMFAS VVRRTGDVNA TAGSANGTQY GRGSQPLPVT IGLSLNNYSS ALMPGQFFVW
     QLTFASGFME IGLSVDGYFY AGTGASTTLI DLIELIDVRP VGPRPSKSTL VFNLGGTANG
     FSYV
//