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Q8JN60 (POLG_BECNB) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 63. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismBovine enteric calicivirus NB (isolate Bovine/United States/Nebraska/1980) (BEC-NB) [Complete proteome]
Taxonomic identifier190239 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNebovirus
Virus hostBos taurus (Bovine) [TaxID: 9913]

Protein attributes

Sequence length2210 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 22102210Genome polyprotein
PRO_0000341628
Chain1 – 302302Protein p34
PRO_0000341629
Chain303 – 645343NTPase
PRO_0000341630
Chain646 – 925280Protein p30
PRO_0000341631
Chain926 – 99065Viral genome-linked protein
PRO_0000341632
Chain991 – 11741843C-like protease
PRO_0000341633
Chain1175 – 1659485RNA-directed RNA polymerase
PRO_0000341634
Chain1660 – 2210551Capsid protein
PRO_0000341635

Regions

Domain426 – 585160SF3 helicase
Domain1010 – 1109100Peptidase C24
Domain1379 – 1501123RdRp catalytic
Nucleotide binding456 – 4638ATP Potential

Sites

Active site10251For 3CLpro activity By similarity
Active site11031For 3CLpro activity Potential
Site302 – 3032Cleavage; by 3CLpro Potential
Site645 – 6462Cleavage; by 3CLpro Potential
Site925 – 9262Cleavage; by 3CLpro Potential
Site990 – 9912Cleavage; by 3CLpro Potential
Site1174 – 11752Cleavage; by 3CLpro Potential
Site1659 – 16602Cleavage; by 3CLpro Potential

Amino acid modifications

Modified residue9401O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q8JN60 [UniParc].

Last modified October 1, 2002. Version 1.
Checksum: 5D499C0C3188839E

FASTA2,210238,639
        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 

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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.
RefSeqNP_663315.1. NC_004064.1.

3D structure databases

ProteinModelPortalQ8JN60.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID951161.

Family and domain databases

Gene3D2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProIPR004005. 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.
IPR009003. Trypsin-like_Pept_dom.
IPR029053. Viral_coat.
[Graphical view]
PfamPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_BECNB
AccessionPrimary (citable) accession number: Q8JN60
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: October 1, 2002
Last modified: July 9, 2014
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries