Q8JN60 (POLG_BECNB) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Genome polyprotein

Cleaved into the following 7 chains:

1. Protein p34
2. NTPase
   EC=3.6.1.15
   Alternative name(s):
   p37
3. Protein p30
4. Viral genome-linked protein
   Alternative name(s):
   VPg
   p8
5. 3C-like protease
   Short name=3CLpro
   EC=3.4.22.66
   Alternative name(s):
   p20
6. RNA-directed RNA polymerase
   Short name=RdRp
   EC=2.7.7.48
   Alternative name(s):
   p53
7. Capsid protein
   Alternative name(s):
   VP1

Gene names

ORF Names:

ORF1

Organism

Bovine enteric calicivirus NB (isolate Bovine/United States/Nebraska/1980) (BEC-NB) [Complete proteome]

Taxonomic identifier

190239 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Nebovirus › Newbury-1 virus

Virus host

Bos taurus (Bovine) [TaxID: 9913]

Protein attributes

Sequence length	2210 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

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 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 codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs By similarity. Capsid protein 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 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).
Subcellular location	Capsid protein: 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 By similarity. 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 By similarity.
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
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 Phosphoprotein
Technical term	Complete proteome
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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 2210	2210	Genome polyprotein		PRO_0000341628
	Chain	1 – 302	302	Protein p34		PRO_0000341629
	Chain	303 – 645	343	NTPase		PRO_0000341630
	Chain	646 – 925	280	Protein p30		PRO_0000341631
	Chain	926 – 990	65	Viral genome-linked protein		PRO_0000341632
	Chain	991 – 1174	184	3C-like protease		PRO_0000341633
	Chain	1175 – 1659	485	RNA-directed RNA polymerase		PRO_0000341634
	Chain	1660 – 2210	551	Capsid protein		PRO_0000341635
Regions
	Domain	426 – 585	160	SF3 helicase
	Domain	1010 – 1109	100	Peptidase C24
	Domain	1379 – 1501	123	RdRp catalytic
	Nucleotide binding	456 – 463	8	ATP Potential
Sites
	Active site	1025	1	For 3CLpro activity By similarity
	Active site	1103	1	For 3CLpro activity Potential
	Site	302 – 303	2	Cleavage; by 3CLpro Potential
	Site	645 – 646	2	Cleavage; by 3CLpro Potential
	Site	925 – 926	2	Cleavage; by 3CLpro Potential
	Site	990 – 991	2	Cleavage; by 3CLpro Potential
	Site	1174 – 1175	2	Cleavage; by 3CLpro Potential
	Site	1659 – 1660	2	Cleavage; by 3CLpro Potential
Amino acid modifications
	Modified residue	940	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q8JN60 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: 5D499C0C3188839E	FASTA	2,210	238,639
	10 20 30 40 50 60 MAPVVSRDQC KPKTPKPHRP APPHRCTTRC PEDCGWYVGR CSCPNVCQRE GWDDFFVADK 70 80 90 100 110 120 VKPPSYVASK TSVADVVDWL LEEDPATDGP SEFDLTQFFQ AYTDKSHQIH RDYAPDQLAQ 130 140 150 160 170 180 ALDMAYILSV DPPDIKLPEY EATRFTHDTS YKGKLPKWLR VYGIKSRELA KKAVTNIRGG 190 200 210 220 230 240 AHWAKGLFKQ MWDSLPGWSE VEAYFKAFFA GIITGVEDAL SKSPSSVWTS LKLTPLLYIW 250 260 270 280 290 300 RNINECSDIA VILGAFWATL ELYNIPSKVY DLVSTALGPM VQELARKVIN VVKGDGSGPK 310 320 330 340 350 360 QEGGRPSFSI PGVLLATFLS AIILGSMPSD GLIKKILRGC ATAAGLVGGF NAVKSIITTV 370 380 390 400 410 420 QGASACKDVK KLASQLMCVT TMAATVSTRG ERQVLASMLN DLNESVRERL VDPAYASLVP 430 440 450 460 470 480 QLSAMSNKIV ELSTMNASAL SAARKRTPAK IIVLCGPPGH GKSVAAHKLA KMLNPNEPSI 490 500 510 520 530 540 WNPFSDHHDE YTAEEVMVID ETPAEPGQWI EDLIAMGSNS PFVPNYDRVE NKTRCFDSKY 550 560 570 580 590 600 VIITTNHNPL INPTHTRAAA LARRLTLVYV NSPDVADFLR QHPGVPPPAT LFKADCSHLH 610 620 630 640 650 660 FDIHPYNSIG TTAIVGHNGT TPVPRAKRVS LEGLCKHVKE MPDREGPPDG VPERMVLVAP 670 680 690 700 710 720 DKGTARFVEA VINTYHNSGL VAQPAAWDTT PQPYQLAVTW QGSNSTVTGQ RWDCNPQTPF 730 740 750 760 770 780 VAPHFTRNMF KRVLGTEVPE YHLLAYACRI TSSSLGDKSL PVPNPTVVIN DPSPTRLALA 790 800 810 820 830 840 LMRHLKNPIA SGLRVVWDLF RGCATGPKRL FTWALSQEWN PMPVTTAFTF PAGTVILHTA 850 860 870 880 890 900 GGVRVVVLPP GPQFGLTEVA RLADHSGQDD PVVPDMFGAT WTELLWRLLK VIGTFLANYG 910 920 930 940 950 960 VAIAGLTLSI AAFKTANKSA KNDRQGWLSG SGVALSDEEY DEWMKYSKKK GKKINADEFL 970 980 990 1000 1010 1020 QLRHRAAMGN DDDDARDYRS FYTAYQLGRE GNNCDDIPLH PAVGPTTGGG YYVHIGNGVG 1030 1040 1050 1060 1070 1080 VTLKHVASGE DVIKELGNDL VKIRTKHHKV GDPAMVVGDG MPVKFVTGHL VVDTRSESVV 1090 1100 1110 1120 1130 1140 FDQTRLNVIR VKVPGLETRR GYCGLPYVNS AGQVVGLHQG SYGVGDKVIT PITPEPTAPP 1150 1160 1170 1180 1190 1200 DTIMWRGLEC ARSDIVTHLP HGTKYSVSPG MKEEATKCSH QPAPLGRNDP RCGQTQVAMV 1210 1220 1230 1240 1250 1260 VKALSPYTGS PAVEKLDGCL VAAISEVRTA IQSLTPKGGF RPLTFAAAWQ SLDLSTSAGA 1270 1280 1290 1300 1310 1320 LAPGKTKRDL CDPDTGMPTG KYKEELLRAW SRAGTGTALD HTYIVALKDE LRPVEKVAEG 1330 1340 1350 1360 1370 1380 KRRLIWGADA RVALIASAAL SPIANALKTV TNLLPVQVGV DPSSASCVSA WVNRLNRHDH 1390 1400 1410 1420 1430 1440 CLELDYSKWD STMSPVLINI AIDILCNTCA SDGLRVAVCQ TLKTRPTALV EGVAVPTKSG 1450 1460 1470 1480 1490 1500 LPSGMPFTSQ INSIVHWILW SATVRKCSLP LNIGSVNELA PFLTYGDDGL YTIPSHLTKS 1510 1520 1530 1540 1550 1560 IDEIVSTLKG YGLSPTAPDK GMNIEIKKTS FTYMSGPVFL KRRIVLTPGG HRALLDLTSL 1570 1580 1590 1600 1610 1620 ARQPVWVNGP RRSVWDHEAQ PIEIDSEVRT IQLQNVLIES AWHQPQDFNQ VAALVYKSAE 1630 1640 1650 1660 1670 1680 ASGITIPRYS LEEARAIYDG RFYGIQHVSM PCNSDLIREG NMSDNKSIPE QQHESSRAMD 1690 1700 1710 1720 1730 1740 AGATGAAAAA PAPPVAAAPA SGLVGALVAE PQSGPSTEQW RTAYTLFGTV SWNANAGPGT 1750 1760 1770 1780 1790 1800 ILTVGRLGPG MNPYTQHIAA MYGGWAGGMD IRITIAGSGF IGGTLAVAAI PPGVDPESVN 1810 1820 1830 1840 1850 1860 VLRMPHVLID ARGGVPLEVT LEDIRTSLYH PMGDANTASL VIAVMTGLIN PLGTDTLSVT 1870 1880 1890 1900 1910 1920 VQLETRPGRD WVFFSLLPPT AGVASADPSQ LLTRVALATS PEVRFGTGVL GILGLPSNPS 1930 1940 1950 1960 1970 1980 VNRVYDVQSR TRGWSFPIPS SSVFMGDARN VEHTRRVMVQ SSAPNNPLSD VFPDGFPDFI 1990 2000 2010 2020 2030 2040 PQSDTEPDGG AVIAGQVLPH PGDNDNFWRL TPVVRGNTTA AINTIPERFN QVYFINLADE 2050 2060 2070 2080 2090 2100 EAVSAATEEL RFNGIQGIFG QRTTARAVQV MQGYVPRAEH IIRPAGFAGV GPQGPNVPIG 2110 2120 2130 2140 2150 2160 FAGTMPNFNA TASGADDLVP VWGPTLVHTA SLLAGTTYEL AENSMYVFSV STSTSTFELG 2170 2180 2190 2200 2210 MLANGTWLGP AQLAGTGITW TEVLSVTYMG MRFAYNPLSG QGIGGESRRL

References

[1]	"Characterization of an enteropathogenic bovine calicivirus representing a potentially new calicivirus genus." Smiley J.R., Chang K.O., Hayes J., Vinje J., Saif L.J. J. Virol. 76:10089-10098(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY082891 Genomic RNA. Translation: AAL99277.1.
RefSeq	NP_663315.1. NC_004064.1.
3D structure databases
ProteinModelPortal	Q8JN60.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	951161.
Family and domain databases
InterPro	IPR004005. Calicivirus_coat. IPR004004. Helic/Pol/Pept_Calicivir-typ. IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR014759. Helicase_SF3_ssRNA_vir. IPR027417. P-loop_NTPase. IPR000317. Peptidase_C24. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. [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.
SUPFAM	SSF52540. SSF52540. 1 hit.
PROSITE	PS50507. RDRP_SSRNA_POS. 1 hit. PS51218. SF3_HELICASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_BECNB

Accession

Primary (citable) accession number: Q8JN60

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 2008
Last sequence update:	October 1, 2002
Last modified:	May 29, 2013
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program