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
//
