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Q288N7

- POLG_BECN1

UniProt

Q288N7 - POLG_BECN1

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Protein
Genome polyprotein
Gene
ORF1
Organism
Bovine enteric calicivirus Newbury agent-1 (isolate Bovine/UK/Newbury1/1976) (BEC)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

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 activityi

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei302 – 3032Cleavage; by 3CLpro Reviewed prediction
Sitei645 – 6462Cleavage; by 3CLpro Reviewed prediction
Sitei925 – 9262Cleavage; by 3CLpro Reviewed prediction
Sitei990 – 9912Cleavage; by 3CLpro Reviewed prediction
Active sitei1025 – 10251For 3CLpro activity By similarity
Active sitei1103 – 11031For 3CLpro activity Reviewed prediction
Sitei1174 – 11752Cleavage; by 3CLpro Reviewed prediction
Sitei1659 – 16602Cleavage; by 3CLpro Reviewed prediction

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi456 – 4638ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. RNA helicase activity Source: InterPro
  4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  5. cysteine-type endopeptidase activity Source: InterPro

GO - Biological processi

  1. RNA-protein covalent cross-linking Source: UniProtKB-KW
  2. transcription, DNA-templated Source: InterPro
  3. viral RNA genome replication Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 7 chains:
Alternative name(s):
p37
Alternative name(s):
VPg
p8
3C-like protease (EC:3.4.22.66)
Short name:
3CLpro
Alternative name(s):
p20
Alternative name(s):
p53
Alternative name(s):
VP1
Gene namesi
ORF Names:ORF1
OrganismiBovine enteric calicivirus Newbury agent-1 (isolate Bovine/UK/Newbury1/1976) (BEC)
Taxonomic identifieri331642 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNebovirus
Virus hostiBos taurus (Bovine) [TaxID: 9913]
ProteomesiUP000000668: Genome

Subcellular locationi

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-SubCell
  2. viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 22102210Genome polyprotein
PRO_0000402448Add
BLAST
Chaini1 – 302302Protein p34 By similarity
PRO_0000402449Add
BLAST
Chaini303 – 645343NTPase By similarity
PRO_0000402450Add
BLAST
Chaini646 – 925280Protein p30 By similarity
PRO_0000402451Add
BLAST
Chaini926 – 99065Viral genome-linked protein By similarity
PRO_0000402452Add
BLAST
Chaini991 – 11741843C-like protease By similarity
PRO_0000402453Add
BLAST
Chaini1175 – 1659485RNA-directed RNA polymerase By similarity
PRO_0000402454Add
BLAST
Chaini1660 – 2210551Capsid protein By similarity
PRO_0000402455Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei940 – 9401O-(5'-phospho-RNA)-tyrosine By similarity

Post-translational modificationi

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.

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini426 – 585160SF3 helicase
Add
BLAST
Domaini1010 – 1109100Peptidase C24
Add
BLAST
Domaini1379 – 1501123RdRp catalytic
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi971 – 9744Poly-Asp
Compositional biasi1686 – 16927Poly-Ala

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR004005. 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]
PfamiPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q288N7-1 [UniParc]FASTAAdd to Basket

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MAPVVSRDRH RHKIPKPHQP APPHRCTVWC PEDCGWYVGR CSCPKSCQRE     50
GWDDFFVADK VKPPSYVASK TSVADVVDWL LEEDPATDGP SEFDLTQFFQ 100
AYTDKSHQIH RDYAPDQLAQ ALDMAYILSV DPPDIKLPEY EATRFTHDTS 150
YKGKLPRWLR VYGFKSRELA KKAITNIKGG AHWAKGLFKQ AWDTLPGWSE 200
VEAYFKAFFA GIITGVEDAL SKSPSSVWTS LKLTPLLYIW RNINECSDIP 250
VILGAFWATL ELYNIPSKVY DLVSTALGPM VQDLARRVIN IIKGDGNGPK 300
QEGGRPSFSI PGVLLATFLS AIILGSMPSD GIIKKVLRGC ATAAGLVGGF 350
NAVKSIITTV QGASACKDVK KLASQLMCVT TMAATVSTRG ERQVLASMLN 400
DLNESVRERL VDPAFAALVP QLSAMSSKIM ELSTINAAAL SAARKRVPAK 450
IVVLCGPPGH GKSVAAHKLA KMLNPNEPSI WNPFSDHHDE YTAEDVVIID 500
ETPAEPGQWV EDLIAMGSNS PFVPNYDRVE NKTRCFDSKY VLITTNHNPL 550
INPTHSRAAA LARRLTWVYV NSPDVADFLR QHPGVAPPAT LFKADCSHLN 600
FDIHPYNSIG TTAVVGHNGT TPLPRAKRTS LEGLCKHIKD LPDREGPPDG 650
VPERMVLVAP DKGTARFVEA VINTYHNSGL VAQPAAWDTT PQKYQLAVTW 700
QGSTSSVVGQ RWDCNPQTPF VAPHFTRNMF KRVLGTEVPE YHLLAYACRI 750
TSSSLGDKSL PVPNPTVVIN DPSPTRLALA LMRHLKNPIA SGLRVVWDLF 800
RGCATGPKRL FTWALSQEWN PMPVTTAFTF PAGTVILHTA GGVRVVVLPP 850
GPQFGLTEVT HLADHSGQDD PVVPDMFGQT WTELLWRLLK VIGTFLANYG 900
VAIAGLTLSI AAFKTANKST RNDRQGWLSG SGVALSDEEY DEWMKYSKKK 950
GKKINADEFL QLRHRAAMGN DDDDARDYRS FYTAYQLGRE GNNCEDLPLH 1000
PAVGPTTGGG YYVHIGNGVG ITLKHVASGE DVIKELGNDL VKIRARHHKM 1050
GDPAMVVGEG APVKFVTGHL VVDARNESVV FDQTRLSVVR VKVPGLETQR 1100
GYCGLPYVNS AGHVVGLHQG SYGVGDKVFT PITDAPAASP DTIMWRGLEC 1150
TRSDIVTHLP HGTKYSISPG MREEAHKCTH QPASLGRNDP RCNQTQVAMV 1200
VKALTPYTSA PAIEKLDPCM VAAITEVRTA IQSLTPKGGF RPLTFAAAWQ 1250
SLDLSTSAGA LAPGKTKRDL CDPDTGMPAG KYREMLLAAW SRAGTGTPLD 1300
HTYIVALKDE LRPVEKVAEG KRRLIWGADA RVALIASAAL TPVANALKTV 1350
TNLLPIQVGV DPSSANCVSS WVGRLQRHDH CLELDYSKWD STMSPVIINI 1400
AIDILCNTCG SDSLRMAVAQ TLKSRPTALV EGVSVPTKSG LPSGMPFTSQ 1450
INSIVHWILW SATVRKCSLP LHIGSVNELA PFLTYGDDGL YTIPSHLTKS 1500
IDEIISTLKG YGLSPTAPDK GANVEIKRTS FTYLSGPVFL KRRIVLTPGG 1550
HRALLDLTSL ARQPVWVNGP RRSVWNHEAQ PIEIDAETRT IQLQNVLIEL 1600
AWHQPQDFDH VLALVVKSAE ASGLTIPRYS QEEARAIYDG RYYGIQHVSL 1650
PNNSDLIREG NMSDNKSTPE QQHESSRAMD AGATGAAAAA PAPPVAAAPA 1700
SGLVGALVAE PQSGPSAEQW RTAYTLFGTV SWNANAGPGT ILTVGRLGPG 1750
MNPYTQHIAA MYGGWAGGMD IRITIAGSGF IGGTLAVAAI PPGVDPESVN 1800
VLRMPHVLID ARGGVPLEVT LEDIRTSLYH PMGDTNTASL VIAVMTGLIN 1850
PLGTDTLSVT VQLETRPGRD WVFFSLLPPT AGVASADPSQ LLTRVALATS 1900
PEVRFGTGVL GILGLPSNPS VNRVYDVQSR TRGWSFPIPS SSVFMGDARN 1950
VEHNRRVMVQ SSAPNNPLSD VFPDGFPDFV PQSDTEPDGG AVIAGQVLPH 2000
PGDNDNFWRL TPVVRGNTTA AINTIPERFN QVYFINLADE EAVSAATEEL 2050
RFNGIQGIFG QRTNARAVQV MQGYVPRAEH IIRPAGFAGV GPQGPNVPIG 2100
FAGTMPNFNA TASGADDLVP VWGPTLVHTA SLLAGTTYEL AENSMYVFSV 2150
STSTSTFELG MLANGTWLGP AQLAGTGITW TEVLSVTYMG MRFAYNPLSG 2200
QGIGGESRRL 2210
Length:2,210
Mass (Da):239,021
Last modified:April 4, 2006 - v1
Checksum:iF05AF2411FE610DE
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DQ013304 Genomic RNA. Translation: AAY60849.1.
RefSeqiYP_529550.1. NC_007916.1.

Genome annotation databases

GeneIDi5130542.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DQ013304 Genomic RNA. Translation: AAY60849.1 .
RefSeqi YP_529550.1. NC_007916.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 5130542.

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
3.40.50.300. 1 hit.
InterProi 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.
IPR009003. Trypsin-like_Pept_dom.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view ]
PRINTSi PR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae."
    Oliver S.L., Asobayire E., Dastjerdi A.M., Bridger J.C.
    Virology 350:240-250(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiPOLG_BECN1
AccessioniPrimary (citable) accession number: Q288N7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2010
Last sequence update: April 4, 2006
Last modified: July 9, 2014
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi