Q86119 (POLG_RHDVA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Genome polyprotein

Alternative name(s):
p254

Cleaved into the following 11 chains:

1. Protein p16
2. Protein p23
3. NTPase
   EC=3.6.1.15
   Alternative name(s):
   2C-like protein
   P2C
   p37
4. Precursor p41
5. Protein p29
6. Protein p23/2
7. Protein p18
8. Viral genome-linked protein
   Alternative name(s):
   VPg
   p13
9. 3C-like protease
   Short name=3CLpro
   EC=3.4.22.66
   Alternative name(s):
   Calicivirin
   Thiol protease P3C
   p15
10. RNA-directed RNA polymerase
    EC=2.7.7.48
    Alternative name(s):
    3Dpol
    p58
11. Capsid protein VP60

Gene names

ORF Names:

ORF1

Organism

Rabbit hemorrhagic disease virus (strain AST89) (Ra/LV/RHDV/AST89/1989/SP) (RHDV-AST89) [Complete proteome]

Taxonomic identifier

314538 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Lagovirus › Rabbit hemorrhagic disease virus

Virus host

Oryctolagus cuniculus (Rabbit) [TaxID: 9986]

Protein attributes

Sequence length	2344 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. 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 encodes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs By similarity. 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.
Catalytic activity	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).
Subunit structure	Binds to histo-blood group antigens at surface of target cells By similarity. Ref.8
Subcellular location	Capsid protein VP60: Virion. Host cytoplasm By similarity.
Post-translational modification	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. Ref.1 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 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.
Sequence similarities	Contains 1 peptidase C24 domain. Contains 1 RdRp catalytic domain. Contains 1 SF3 helicase domain.

Ontologies

Keywords
Biological process	Viral RNA replication
Cellular component	Host cytoplasm Virion
Coding sequence diversity	Alternative promoter usage
Ligand	ATP-binding Nucleotide-binding
Molecular function	Capsid protein Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
PTM	Covalent protein-RNA linkage Disulfide bond Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological_process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative promoter usage. [Align] [Select]

Isoform Genome polyprotein (identifier: Q86119-1)

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.

Note: Produced from the genomic RNA.

Isoform Subgenomic capsid protein VP60 (identifier: Q86119-2)

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.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 2344	2344	Genome polyprotein		PRO_0000341999
	Chain	1 – 143	143	Protein p16 By similarity		PRO_0000036941
	Chain	144 – 339	196	Protein p23 By similarity		PRO_0000036942
	Chain	340 – 718	379	NTPase By similarity		PRO_0000036943
	Chain	712 – 1108	397	Precursor p41 By similarity		PRO_0000342000
	Chain	712 – 936	225	Protein p23/2 By similarity		PRO_0000342001
	Chain	719 – 993	275	Protein p29 By similarity		PRO_0000036944
	Chain	937 – 1108	172	Protein p18 By similarity		PRO_0000342002
	Chain	994 – 1108	115	Viral genome-linked protein By similarity		PRO_0000036945
	Chain	1109 – 1251	143	3C-like protease By similarity		PRO_0000036946
	Chain	1252 – 1767	516	RNA-directed RNA polymerase By similarity		PRO_0000036947
	Chain	1768 – 2344	577	Capsid protein VP60 By similarity		PRO_0000036949
Regions
	Domain	492 – 653	162	SF3 helicase
	Domain	1120 – 1218	99	Peptidase C24
	Domain	1495 – 1619	125	RdRp catalytic
	Nucleotide binding	522 – 529	8	ATP Potential
Sites
	Active site	1135	1	For 3CLpro activity By similarity
	Active site	1159	1	For 3CLpro activity By similarity
	Active site	1212	1	For 3CLpro activity Potential
	Site	143 – 144	2	Cleavage; by 3CLpro By similarity
	Site	339 – 340	2	Cleavage; by 3CLpro By similarity
	Site	718 – 719	2	Cleavage; by 3CLpro By similarity
	Site	936 – 937	2	Cleavage; by host By similarity
	Site	993 – 994	2	Cleavage; by 3CLpro By similarity
	Site	1108 – 1109	2	Cleavage; by 3CLpro By similarity
	Site	1251 – 1252	2	Cleavage; by 3CLpro By similarity
	Site	1767 – 1768	2	Cleavage; by 3CLpro By similarity
Amino acid modifications
	Modified residue	1014	1	O-(5'-phospho-RNA)-tyrosine
	Disulfide bond	1584 ↔ 1591		By similarity
Natural variations
	Alternative sequence	1 – 1765	1765	Missing in isoform Subgenomic capsid protein VP60.		VSP_034379
Experimental info
	Mutagenesis	1767	1	E → G: Loss of cleavage between RNA-directed RNA polymerase and VP60. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform Genome polyprotein [UniParc]. Last modified October 1, 2003. Version 2. Checksum: E1C61F038111F092	FASTA	2,344	256,817
	10 20 30 40 50 60 MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFLGQ NGKEGPLETC 70 80 90 100 110 120 NKCGKWLNGF GCFGLEDLGD VCLCSIAQQK HKFGPVCLCN RAYIHDCGRW RRRSRFLKHY 130 140 150 160 170 180 KALNKVIPCA YQFDESFSTP VFEGEVDDLF VELGAPTSMG FMDKKLLKKG KKLMDKFVDV 190 200 210 220 230 240 DEPCLTSRDA SLLDSIASDN TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV 250 260 270 280 290 300 TWYTKLGNIT EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV 310 320 330 340 350 360 NLLAILMDWT NDLTGFVTTL VRLLELYGVV QATVNLIVEG VKSFWDKVVC ATDRCFDLLK 370 380 390 400 410 420 RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT TFMKGAGKLT TFAGVIGAIR 430 440 450 460 470 480 TLWITINQHM VAKDLTSIQQ KVMTVVKMAN EAATLDQLEI VSCLCSDLEN TLTNRCTLPS 490 500 510 520 530 540 YNQHLGILNA SQKVISDLHT MVLGKINMTK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG 550 560 570 580 590 600 CQHPSTINFG LDHFDSYTGE EVAIADEFNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK 610 620 630 640 650 660 NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR HGSKPGRSCY 670 680 690 700 710 720 SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY SELLDLIKSE HPDVASFEGA 730 740 750 760 770 780 NRFNFVYPDA QYDQALLMWK QYFVMYGCVA RLAKNFVDDI PYNQVHISRA SDPKIEGCVE 790 800 810 820 830 840 YQCKFQHLWR MVPQFVLGCV NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILPFHSQT 850 860 870 880 890 900 TLINPSFIKL IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDDPV 910 920 930 940 950 960 STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL ISGFSWRQIA 970 980 990 1000 1010 1020 HLFVEVISHL CANHLVNLAT MAALGAVATK AFQGVKGKTK RGRGARVNLG NDEYDEWQAA 1030 1040 1050 1060 1070 1080 RREFVNAHDM TAEEYLAMKN KAAMGSDDQD SVMFRSWWTR RQLRPDEDQV TVVGRGGVRN 1090 1100 1110 1120 1130 1140 EVIRTRVRQT PKGPKTLDDG GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS 1150 1160 1170 1180 1190 1200 CSEVVTCSPT TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA 1210 1220 1230 1240 1250 1260 YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY ETSNFFCGEP 1270 1280 1290 1300 1310 1320 IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPEEYKTGYR PANLGRSDPD SDKSLMNIAV 1330 1340 1350 1360 1370 1380 KNLQVYQQEP KLDKVDEFIE RAAADVLGYL RFLTKGERQA NLNFKAAFNT LDLSTSCGPF 1390 1400 1410 1420 1430 1440 VPGKKIDHVK DGVMDQVHAK HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL 1450 1460 1470 1480 1490 1500 LWGCDVGVAV CAAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL 1510 1520 1530 1540 1550 1560 DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI VQTKRGLPSG 1570 1580 1590 1600 1610 1620 MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF YTYGDDGVYA MTPMMVSLLP 1630 1640 1650 1660 1670 1680 AIIENLRDYG LSPTAADKTE FIDVCPLNKI SFLKRTFELT DIGWVSKLDK SSILRQLEWS 1690 1700 1710 1720 1730 1740 KTTSRHMMIE ETYDLAKEER GVQLEELQVA AAAHGQEFFN FVCKELERQQ AYTQFSVYSY 1750 1760 1770 1780 1790 1800 DAARKILADR KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGMDPGVV 1810 1820 1830 1840 1850 1860 ATTSVVTAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA PGSILYTVQH 1870 1880 1890 1900 1910 1920 SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVA AVIPPGIEIG PGLEVRQFPH 1930 1940 1950 1960 1970 1980 VVIDARSLEP VTITMPDLRP NMYHPTGDPG LVPTLVLSVY NNLINPFGGS TSAIQVTVET 1990 2000 2010 2020 2030 2040 RPSEDFEFVM IRAPSSKTVD SISPAGLLTT PVLTGVGNDN RWNGQIVGLQ PVPGGFSTCN 2050 2060 2070 2080 2090 2100 RHWNLNGSTY GWSSPRFADI DHRRGSASYP GNNATNVLQF WYANAGSAID NPISQVAPDG 2110 2120 2130 2140 2150 2160 FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP GNLQPTTNTS 2170 2180 2190 2200 2210 2220 GSQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPSANAIT YTPQPDRIVT TPGTPAAAPV 2230 2240 2250 2260 2270 2280 GKNTPIMFAS VVRRTGDVNA TAGSANGTQY GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW 2290 2300 2310 2320 2330 2340 QLTFASGFME IGLSVDGYFY AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG FSYV
	Isoform Subgenomic capsid protein VP60 (VP1) [UniParc]. Checksum: 7BA463B7C7D77BAC	FASTA	579	60,241
	10 20 30 40 50 60 MEGKARTAPQ GEAAGTATTA SVPGTTTDGM DPGVVATTSV VTAENSSASI ATAGIGGPPQ 70 80 90 100 110 120 QVDQQETWRT NFYYNDVFTW SVADAPGSIL YTVQHSPQNN PFTAVLSQMY AGWAGGMQFR 130 140 150 160 170 180 FIVAGSGVFG GRLVAAVIPP GIEIGPGLEV RQFPHVVIDA RSLEPVTITM PDLRPNMYHP 190 200 210 220 230 240 TGDPGLVPTL VLSVYNNLIN PFGGSTSAIQ VTVETRPSED FEFVMIRAPS SKTVDSISPA 250 260 270 280 290 300 GLLTTPVLTG VGNDNRWNGQ IVGLQPVPGG FSTCNRHWNL NGSTYGWSSP RFADIDHRRG 310 320 330 340 350 360 SASYPGNNAT NVLQFWYANA GSAIDNPISQ VAPDGFPDMS FVPFNGPGIP AAGWVGFGAI 370 380 390 400 410 420 WNSNSGAPNV TTVQAYELGF ATGAPGNLQP TTNTSGSQTV AKSIYAVVTG TAQNPAGLFV 430 440 450 460 470 480 MASGVISTPS ANAITYTPQP DRIVTTPGTP AAAPVGKNTP IMFASVVRRT GDVNATAGSA 490 500 510 520 530 540 NGTQYGTGSQ PLPVTIGLSL NNYSSALMPG QFFVWQLTFA SGFMEIGLSV DGYFYAGTGA 550 560 570 STTLIDLTEL IDVRPVGPRP SKSTLVFNLG GTANGFSYV

References

[1]	"Processing of rabbit hemorrhagic disease virus polyprotein." Martin-Alonso J.M., Casais R., Boga J.A., Parra F. J. Virol. 70:1261-1265(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], PROTEIN SEQUENCE OF 719-724 AND 1009-1114, MUTAGENESIS OF GLU-1767, PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[2]	Casais R., Martin-Alonso J.M., Boga J.A., Parra F. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 1891; 2058 AND 2061.
[3]	"Molecular cloning, sequence and expression of the capsid protein gene from rabbit hemorrhagic disease virus (Spanish isolate AST/89)." Boga J.A., Casais R., Marin M.S., Martin-Alonso J.M., Carmenes R., Prieto M., Parra F. J. Gen. Virol. 75:2409-2413(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1650-2344.
[4]	"The amino terminal sequence of VP60 from rabbit hemorrhagic disease virus supports its putative subgenomic origin." Parra F., Boga J.A., Marin M.S., Casais R. Virus Res. 27:219-228(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1766-1797, PROTEIN SEQUENCE OF 1767-1780.
[5]	"In vitro translation of a subgenomic mRNA from purified virions of the Spanish field isolate AST/89 of rabbit hemorrhagic disease virus (RHDV)." Boga J.A., Marin M.S., Casais R., Prieto M., Parra F. Virus Res. 26:33-40(1992) [PubMed] [Europe PMC] [Abstract] Cited for: SUBGENOMIC ORIGIN OF VP60.
[6]	"Identification of the amino acid residue involved in rabbit hemorrhagic disease virus VPg uridylylation." Machin A., Martin Alonso J.M., Parra F. J. Biol. Chem. 276:27787-27792(2001) [PubMed] [Europe PMC] [Abstract] Cited for: COVALENT RNA-LINKAGE OF VPG, URIDYLYLATION AT TYR-1014.
[7]	"Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA by internal initiation on (-)sense genomic RNA: mapping of a subgenomic promoter." Morales M., Barcena J., Ramirez M.A., Boga J.A., Parra F., Torres J.M. J. Biol. Chem. 279:17013-17018(2004) [PubMed] [Europe PMC] [Abstract] Cited for: SUBGENOMIC ORIGIN OF VP60.
[8]	"NMR experiments reveal the molecular basis of receptor recognition by a calicivirus." Rademacher C., Krishna N.R., Palcic M., Parra F., Peters T. J. Am. Chem. Soc. 130:3669-3675(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION OF VP60 WITH HISTO-BLOOD GROUP ANTIGENS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z49271 Genomic RNA. Translation: CAA89265.2.
Z49271 Genomic RNA. Translation: CAD91718.1.
Z24757 Genomic RNA. Translation: CAA80881.1. Sequence problems.
Z24757 Genomic RNA. Translation: CAA80883.1. Sequence problems.
X73046 mRNA. Translation: CAA51524.1.

PIR

S64740.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3ZUE	electron microscopy	10.30	A/B/C	1766-2344	[»]

ProteinModelPortal

Q86119.

SMR

Q86119. Positions 1256-1752.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR003593. AAA+_ATPase.
IPR004005. Calicivirus_coat.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR000317. Peptidase_C24.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]

Pfam

PF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]

PRINTS

PR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.

SMART

SM00382. AAA. 1 hit.
[Graphical view]

SUPFAM

SSF50494. Pept_Ser_Cys. 1 hit.

PROSITE

PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

POLG_RHDVA

Accession

Primary (citable) accession number: Q86119
Secondary accession number(s): Q7THT7 , Q86123, Q86124, Q9IBM0

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	October 1, 2003
Last modified:	May 1, 2013
This is version 81 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program