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Genome polyprotein (p254) [Cleaved into: Protein p16; Protein p23; NTPase (EC 3.6.1.15) (2C-like protein) (P2C) (p37); Precursor p41; Protein p29; Protein p23/2; Protein p18; Viral genome-linked protein (VPg) (p13); 3C-like protease (3CLpro) (EC 3.4.22.66) (Calicivirin) (Thiol protease P3C) (p15); RNA-directed RNA polymerase (EC 2.7.7.48) (3Dpol) (p58); Capsid protein VP60]

 POLG_RHDVA              Reviewed;        2344 AA.
Q86119; Q7THT7; Q86123; Q86124; Q9IBM0;
29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
01-OCT-2003, sequence version 2.
25-OCT-2017, entry version 105.
RecName: Full=Genome polyprotein;
AltName: Full=p254;
Contains:
RecName: Full=Protein p16;
Contains:
RecName: Full=Protein p23;
Contains:
RecName: Full=NTPase;
EC=3.6.1.15;
AltName: Full=2C-like protein;
AltName: Full=P2C;
AltName: Full=p37;
Contains:
RecName: Full=Precursor p41;
Contains:
RecName: Full=Protein p29;
Contains:
RecName: Full=Protein p23/2;
Contains:
RecName: Full=Protein p18;
Contains:
RecName: Full=Viral genome-linked protein;
AltName: Full=VPg;
AltName: Full=p13;
Contains:
RecName: Full=3C-like protease;
Short=3CLpro;
EC=3.4.22.66;
AltName: Full=Calicivirin;
AltName: Full=Thiol protease P3C;
AltName: Full=p15;
Contains:
RecName: Full=RNA-directed RNA polymerase;
EC=2.7.7.48;
AltName: Full=3Dpol;
AltName: Full=p58;
Contains:
RecName: Full=Capsid protein VP60;
ORFNames=ORF1;
Rabbit hemorrhagic disease virus (strain AST89)
(Ra/LV/RHDV/AST89/1989/SP) (RHDV-AST89).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Caliciviridae; Lagovirus.
NCBI_TaxID=314538;
NCBI_TaxID=9986; Oryctolagus cuniculus (Rabbit).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA], PROTEIN SEQUENCE OF 719-724 AND
1009-1114, MUTAGENESIS OF GLU-1767, AND PROTEOLYTIC PROCESSING OF
POLYPROTEIN.
PubMed=8551592;
Martin-Alonso J.M., Casais R., Boga J.A., Parra F.;
"Processing of rabbit hemorrhagic disease virus polyprotein.";
J. Virol. 70:1261-1265(1996).
[2]
SEQUENCE REVISION TO 1891; 2058 AND 2061.
Casais R., Martin-Alonso J.M., Boga J.A., Parra F.;
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1650-2344.
PubMed=8077941; DOI=10.1099/0022-1317-75-9-2409;
Boga J.A., Casais R., Marin M.S., Martin-Alonso J.M., Carmenes R.,
Prieto M., Parra F.;
"Molecular cloning, sequence and expression of the capsid protein gene
from rabbit hemorrhagic disease virus (Spanish isolate AST/89).";
J. Gen. Virol. 75:2409-2413(1994).
[4]
NUCLEOTIDE SEQUENCE [MRNA] OF 1766-1797, AND PROTEIN SEQUENCE OF
1767-1780.
PubMed=8488721; DOI=10.1016/0168-1702(93)90034-K;
Parra F., Boga J.A., Marin M.S., Casais R.;
"The amino terminal sequence of VP60 from rabbit hemorrhagic disease
virus supports its putative subgenomic origin.";
Virus Res. 27:219-228(1993).
[5]
SUBGENOMIC ORIGIN OF VP60.
PubMed=1441736; DOI=10.1016/0168-1702(92)90144-X;
Boga J.A., Marin M.S., Casais R., Prieto M., Parra F.;
"In vitro translation of a subgenomic mRNA from purified virions of
the Spanish field isolate AST/89 of rabbit hemorrhagic disease virus
(RHDV).";
Virus Res. 26:33-40(1992).
[6]
COVALENT RNA LINKAGE AT TYR-1014 (VPG), AND URIDYLYLATION AT TYR-1014.
PubMed=11369764; DOI=10.1074/jbc.M100707200;
Machin A., Martin Alonso J.M., Parra F.;
"Identification of the amino acid residue involved in rabbit
hemorrhagic disease virus VPg uridylylation.";
J. Biol. Chem. 276:27787-27792(2001).
[7]
SUBGENOMIC ORIGIN OF VP60.
PubMed=14744857; DOI=10.1074/jbc.M313674200;
Morales M., Barcena J., Ramirez M.A., Boga J.A., Parra F.,
Torres J.M.;
"Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA
by internal initiation on (-)sense genomic RNA: mapping of a
subgenomic promoter.";
J. Biol. Chem. 279:17013-17018(2004).
[8]
INTERACTION OF VP60 WITH HISTO-BLOOD GROUP ANTIGENS.
PubMed=18302385; DOI=10.1021/ja710854r;
Rademacher C., Krishna N.R., Palcic M., Parra F., Peters T.;
"NMR experiments reveal the molecular basis of receptor recognition by
a calicivirus.";
J. Am. Chem. Soc. 130:3669-3675(2008).
-!- FUNCTION: NTPase presumably plays a role in replication.
{ECO:0000250}.
-!- FUNCTION: 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). {ECO:0000250}.
-!- FUNCTION: 3C-like protease processes the polyprotein: 3CLpro-RdRp
(p72) is first released by autocleavage, then all other proteins
are cleaved. {ECO:0000250}.
-!- FUNCTION: 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). {ECO:0000255|PROSITE-ProRule:PRU00539}.
-!- FUNCTION: 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). {ECO:0000250}.
-!- CATALYTIC ACTIVITY: NTP + H(2)O = NDP + phosphate.
-!- CATALYTIC ACTIVITY: Endopeptidase with a preference for cleavage
when the P1 position is occupied by Glu-|-Xaa and the P1' position
is occupied by Gly-|-Yaa.
-!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
+ RNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00539}.
-!- SUBUNIT: Binds to histo-blood group antigens at surface of target
cells. {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Capsid protein VP60: Virion. Host cytoplasm
{ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative promoter usage; Named isoforms=2;
Name=Genome polyprotein;
IsoId=Q86119-1; Sequence=Displayed;
Note=Produced from the genomic RNA.;
Name=Subgenomic capsid protein VP60; Synonyms=VP1;
IsoId=Q86119-2; Sequence=VSP_034379;
Note=Produced from the subgenomic RNA.;
-!- PTM: 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).
{ECO:0000250}.
-!- PTM: 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.
-!- MISCELLANEOUS: Two different 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.
-----------------------------------------------------------------------
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EMBL; Z49271; CAA89265.2; -; Genomic_RNA.
EMBL; Z49271; CAD91718.1; -; Genomic_RNA.
EMBL; Z24757; CAA80881.1; ALT_SEQ; Genomic_RNA.
EMBL; Z24757; CAA80883.1; ALT_SEQ; Genomic_RNA.
EMBL; X73046; CAA51524.1; -; mRNA.
PIR; S64740; S64740.
PDB; 3ZUE; EM; 10.30 A; A/B/C=1766-2344.
PDBsum; 3ZUE; -.
ProteinModelPortal; Q86119; -.
SMR; Q86119; -.
OrthoDB; VOG090000BA; -.
Proteomes; UP000008653; Genome.
GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0019028; C:viral capsid; IEA:UniProtKB-KW.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
GO; GO:0003723; F:RNA binding; IEA:InterPro.
GO; GO:0003724; F:RNA helicase activity; IEA:InterPro.
GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
CDD; cd00205; rhv_like; 1.
InterPro; IPR004005; Calicivirus_coat.
InterPro; IPR004004; Helic/Pol/Pept_Calicivir-typ.
InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
InterPro; IPR014759; Helicase_SF3_ssRNA_vir.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR000317; Peptidase_C24.
InterPro; IPR009003; Peptidase_S1_PA.
InterPro; IPR033703; Rhv-like.
InterPro; IPR001205; RNA-dir_pol_C.
InterPro; IPR007094; RNA-dir_pol_PSvirus.
Pfam; PF00915; Calici_coat; 1.
Pfam; PF03510; Peptidase_C24; 1.
Pfam; PF00680; RdRP_1; 1.
Pfam; PF00910; RNA_helicase; 1.
PRINTS; PR00916; 2CENDOPTASE.
PRINTS; PR00918; CALICVIRUSNS.
SUPFAM; SSF50494; SSF50494; 1.
SUPFAM; SSF52540; SSF52540; 1.
PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PROSITE; PS51218; SF3_HELICASE_2; 1.
1: Evidence at protein level;
3D-structure; Alternative promoter usage; ATP-binding; Capsid protein;
Complete proteome; Covalent protein-RNA linkage;
Direct protein sequencing; Disulfide bond; Helicase; Host cytoplasm;
Hydrolase; Nucleotide-binding; Nucleotidyltransferase; Phosphoprotein;
Protease; RNA-directed RNA polymerase; Thiol protease; Transferase;
Viral RNA replication; Virion.
CHAIN 1 2344 Genome polyprotein.
/FTId=PRO_0000341999.
CHAIN 1 143 Protein p16. {ECO:0000250}.
/FTId=PRO_0000036941.
CHAIN 144 339 Protein p23. {ECO:0000250}.
/FTId=PRO_0000036942.
CHAIN 340 718 NTPase. {ECO:0000250}.
/FTId=PRO_0000036943.
CHAIN 712 1108 Precursor p41. {ECO:0000250}.
/FTId=PRO_0000342000.
CHAIN 712 936 Protein p23/2. {ECO:0000250}.
/FTId=PRO_0000342001.
CHAIN 719 993 Protein p29. {ECO:0000250}.
/FTId=PRO_0000036944.
CHAIN 937 1108 Protein p18. {ECO:0000250}.
/FTId=PRO_0000342002.
CHAIN 994 1108 Viral genome-linked protein.
{ECO:0000250}.
/FTId=PRO_0000036945.
CHAIN 1109 1251 3C-like protease. {ECO:0000250}.
/FTId=PRO_0000036946.
CHAIN 1252 1767 RNA-directed RNA polymerase.
{ECO:0000250}.
/FTId=PRO_0000036947.
CHAIN 1768 2344 Capsid protein VP60. {ECO:0000250}.
/FTId=PRO_0000036949.
DOMAIN 492 653 SF3 helicase. {ECO:0000255|PROSITE-
ProRule:PRU00551}.
DOMAIN 1120 1218 Peptidase C24.
DOMAIN 1495 1619 RdRp catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00539}.
NP_BIND 522 529 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00551}.
ACT_SITE 1135 1135 For 3CLpro activity. {ECO:0000250}.
ACT_SITE 1159 1159 For 3CLpro activity. {ECO:0000250}.
ACT_SITE 1212 1212 For 3CLpro activity. {ECO:0000255}.
SITE 143 144 Cleavage; by 3CLpro. {ECO:0000250}.
SITE 339 340 Cleavage; by 3CLpro. {ECO:0000250}.
SITE 718 719 Cleavage; by 3CLpro. {ECO:0000250}.
SITE 936 937 Cleavage; by host. {ECO:0000250}.
SITE 993 994 Cleavage; by 3CLpro. {ECO:0000250}.
SITE 1108 1109 Cleavage; by 3CLpro. {ECO:0000250}.
SITE 1251 1252 Cleavage; by 3CLpro. {ECO:0000250}.
SITE 1767 1768 Cleavage; by 3CLpro. {ECO:0000250}.
MOD_RES 1014 1014 O-(5'-phospho-RNA)-tyrosine.
{ECO:0000269|PubMed:11369764}.
MOD_RES 1014 1014 O-UMP-tyrosine; transient.
{ECO:0000269|PubMed:11369764}.
DISULFID 1584 1591 {ECO:0000250}.
VAR_SEQ 1 1765 Missing (in isoform Subgenomic capsid
protein VP60). {ECO:0000305}.
/FTId=VSP_034379.
MUTAGEN 1767 1767 E->G: Loss of cleavage between RNA-
directed RNA polymerase and VP60.
{ECO:0000269|PubMed:8551592}.
SEQUENCE 2344 AA; 256817 MW; E1C61F038111F092 CRC64;
MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFLGQ NGKEGPLETC
NKCGKWLNGF GCFGLEDLGD VCLCSIAQQK HKFGPVCLCN RAYIHDCGRW RRRSRFLKHY
KALNKVIPCA YQFDESFSTP VFEGEVDDLF VELGAPTSMG FMDKKLLKKG KKLMDKFVDV
DEPCLTSRDA SLLDSIASDN TIRAKLEEEY 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 TQQQLDRITN GVEGVTVTTV NNILPFHSQT
TLINPSFIKL IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDDPV
STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL ISGFSWRQIA
HLFVEVISHL CANHLVNLAT MAALGAVATK AFQGVKGKTK RGRGARVNLG NDEYDEWQAA
RREFVNAHDM TAEEYLAMKN KAAMGSDDQD SVMFRSWWTR RQLRPDEDQV TVVGRGGVRN
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 RFLTKGERQA NLNFKAAFNT LDLSTSCGPF
VPGKKIDHVK DGVMDQVHAK HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL
LWGCDVGVAV CAAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL
DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI VQTKRGLPSG
MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF YTYGDDGVYA MTPMMVSLLP
AIIENLRDYG LSPTAADKTE FIDVCPLNKI SFLKRTFELT DIGWVSKLDK SSILRQLEWS
KTTSRHMMIE ETYDLAKEER GVQLEELQVA AAAHGQEFFN FVCKELERQQ 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 GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW
QLTFASGFME IGLSVDGYFY AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG
FSYV


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