ID   POLG_RHDVB              Reviewed;        2344 AA.
AC   Q89273;
DT   29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   24-JAN-2024, entry version 118.
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 BS89) (Ra/LV/RHDV/BS89/1989/IT)
OS   (RHDV-BS89).
OC   Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC   Picornavirales; Caliciviridae; Lagovirus; Rabbit hemorrhagic disease virus.
OX   NCBI_TaxID=314537;
OH   NCBI_TaxID=9986; Oryctolagus cuniculus (Rabbit).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA], AND CHARACTERIZATION OF 3C-LIKE
RP   PROTEASE.
RX   PubMed=8083986; DOI=10.1128/jvi.68.10.6487-6495.1994;
RA   Boniotti B., Wirblich C., Sibilia M., Meyers G., Thiel H.J., Rossi C.;
RT   "Identification and characterization of a 3C-like protease from rabbit
RT   hemorrhagic disease virus, a calicivirus.";
RL   J. Virol. 68:6487-6495(1994).
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=Q89273-1; Sequence=Displayed;
CC       Name=Subgenomic capsid protein VP60; Synonyms=VP1;
CC         IsoId=Q89273-2; Sequence=VSP_034380;
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; X87607; CAA60910.1; -; Genomic_RNA.
DR   PIR; S55399; S55399.
DR   SMR; Q89273; -.
DR   MEROPS; C24.001; -.
DR   Proteomes; UP000140996; 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   1: Evidence at protein level;
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_0000342003"
FT   CHAIN           1..143
FT                   /note="Protein p16"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036950"
FT   CHAIN           144..339
FT                   /note="Protein p23"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036951"
FT   CHAIN           340..718
FT                   /note="NTPase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036952"
FT   CHAIN           719..1108
FT                   /note="Precursor p41"
FT                   /id="PRO_0000342004"
FT   CHAIN           719..993
FT                   /note="Protein p29"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036953"
FT   CHAIN           719..936
FT                   /note="Protein p23/2"
FT                   /id="PRO_0000342005"
FT   CHAIN           937..1108
FT                   /note="Protein p18"
FT                   /id="PRO_0000342006"
FT   CHAIN           994..1108
FT                   /note="Viral genome-linked protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036954"
FT   CHAIN           1109..1251
FT                   /note="3C-like protease"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036955"
FT   CHAIN           1252..1767
FT                   /note="RNA-directed RNA polymerase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036956"
FT   CHAIN           1768..2344
FT                   /note="Capsid protein VP60"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036958"
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..1794
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_034380"
SQ   SEQUENCE   2344 AA;  256898 MW;  B92411C5067EB0C2 CRC64;
     MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFPGQ NGKEGPLKTC
     NKCGKWLNGF GYFGLEDLGD VCLCSIAQQK HKFGPVCLCN RAYIHDCGRW RRRSRFLKHY
     KALNKVIPCA YQFDESFSTP VFEGEVDDLF VELGAPTSMG FMDKKLLKKG KKLMDKFVDV
     DEPCLTSRDA SLLDSIASDT TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV
     TWYTKLGNIT EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV
     NLLAILMDWT NDLAGFVTTL VRLLELYGVV QATVNLIIEG VKSFWDKVVC ATERCFDLLK
     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 HGSKPGKSCY
     SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY SELLDLIKSE HPDVASFDGA
     NRFNFVYPDA QYDQALLMWK QYFVMYGCVA RLAKNFVDDI PYNQVHISRA SDPKIEGCVE
     YQCKFQHLWR MVPQFVLGCV NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILAFHSQT
     TLINPSFLKL IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDEPV
     STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL ISGFSWRQIA
     HLFVEVISHL CANHLVNLAT MAALGPVATK AFQGVKGKTK RGRGARVNLG NDEYDEWQAA
     RREFVNAHDM TAEEYLAMKN KAAMGSDDQD SVMFRSWWTR RQLRPDEDQV TIVGRGGVRN
     EVIRTRVRQT PKGPKTLDDG GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS
     CSEIVTCSPT TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA
     YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY ETSNFFCGEP
     IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPDEYKTGYR PANLGRSDPD SDKSLMNIAV
     KNLQVYQQEP KLDKVDEFIE RAAADVLGYL RFLTKGERQA NLNFKAAFNT LDLSTSCGPF
     VPGKKIDHVK DGVMDQVLAK HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVREGKKRL
     LWGCDVGVAV CRAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL
     DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI VQTKRGLPSG
     MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF YTYGDDGVYA MTPMMVSLLP
     AIIENLRDYG LSPTAADKTE FIDVCPLNKI SFLKRTFELT DIGWVSKLDK SSILRQLEWS
     KTTSRHMMIE ETYDLAKEER GVQLEELQVP AAAHGQEFFN FVCKELERQQ AYTQFSVYSY
     DAARKILADR KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGLDPGVV
     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 GSNATNVLQF WYANAGSAVD NPISQVAPDG
     FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP GNLQPTTNTS
     GAQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPNANAIT YTPQPDRIVT TPGTPAAAPV
     GKNTPIMFAS VVRRTGDVNA TAGSANGTQY GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW
     QLTFASGFME IGLSVDGYFY AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG
     FSYV
//