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Q9YLS4

- POLG_AEVCA

UniProt

Q9YLS4 - POLG_AEVCA

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Protein

Genome polyprotein

Gene
N/A
Organism
Avian encephalomyelitis virus (strain Calnek vaccine) (AEV)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at transcript leveli

Functioni

Capsid proteins VP1, VP2, and VP3 form a closed capsid enclosing the viral positive strand RNA genome. All these proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes By similarity.
Protein VP0: VP0 precursor is a component of immature procapsids. The N-terminal domain of VP0, protein VP4, is needed for the assembly of 12 pentamers into the icosahedral structure. Unlike other picornaviruses, AEV VP4 may not be myristoylated By similarity.
Protein 2B and 2BC precursor affect membrane integrity and cause an increase in membrane permeability By similarity.
Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities By similarity.
Protein 3A, via its hydrophobic domain, serves as membrane anchor By similarity.
Protein 3B is covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. It acts as a genome-linked replication primer By similarity.
Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease By similarity.
RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals By similarity.

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
NTP + H2O = NDP + phosphate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei19 – 202Cleavage Reviewed prediction
Sitei242 – 2432Cleavage; by protease 3C Reviewed prediction
Sitei487 – 4882Cleavage; by protease 3C Reviewed prediction
Sitei757 – 7582Cleavage; by host Reviewed prediction
Sitei806 – 8072Cleavage; by protease 3C By similarity
Sitei1021 – 10222Cleavage; by protease 3C Reviewed prediction
Sitei1347 – 13482Cleavage; by protease 3C Reviewed prediction
Sitei1412 – 14132Cleavage; by protease 3C Reviewed prediction
Sitei1433 – 14342Cleavage; by protease 3C Reviewed prediction
Active sitei1477 – 14771For protease 3C activity By similarity
Active sitei1515 – 15151For protease 3C activity By similarity
Active sitei1603 – 16031For protease 3C activity By similarity
Sitei1648 – 16492Cleavage; by protease 3C By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1153 – 11608ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. cysteine-type endopeptidase activity Source: InterPro
  3. ion channel activity Source: UniProtKB-KW
  4. RNA binding Source: UniProtKB-KW
  5. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  6. RNA helicase activity Source: InterPro
  7. structural molecule activity Source: InterPro

GO - Biological processi

  1. pore formation by virus in membrane of host cell Source: UniProtKB-KW
  2. protein oligomerization Source: UniProtKB-KW
  3. RNA-protein covalent cross-linking Source: UniProtKB-KW
  4. suppression by virus of host RIG-I activity by RIG-I proteolysis Source: UniProtKB
  5. transcription, DNA-templated Source: InterPro
  6. viral entry into host cell Source: UniProtKB-KW
  7. viral RNA genome replication Source: InterPro
  8. virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Ion channel, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase, Viral ion channel

Keywords - Biological processi

Host-virus interaction, Ion transport, Transport, Viral attachment to host cell, Viral RNA replication, Virus entry into host cell

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 12 chains:
Alternative name(s):
VP4-VP2
Alternative name(s):
P1A
Virion protein 4
Alternative name(s):
P1B
Virion protein 2
Alternative name(s):
P1C
Virion protein 3
Alternative name(s):
P1D
Virion protein 1
Protein 2A
Short name:
P2A
Protein 2B
Short name:
P2B
Protein 2C (EC:3.6.1.15)
Short name:
P2C
Protein 3A
Short name:
P3A
Protein 3B
Short name:
P3B
Alternative name(s):
VPg
Protease 3C (EC:3.4.22.28)
Short name:
P3C
Alternative name(s):
Picornain 3C
OrganismiAvian encephalomyelitis virus (strain Calnek vaccine) (AEV)
Taxonomic identifieri475778 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeTremovirus
Virus hostiAnas (ducks) [TaxID: 8835]
Gallus gallus (Chicken) [TaxID: 9031]
Phasianidae [TaxID: 9005]
ProteomesiUP000000357: Genome

Subcellular locationi

Chain Protein VP2 : Virion. Host cytoplasm Reviewed prediction
Chain Protein VP3 : Virion. Host cytoplasm Reviewed prediction
Chain Protein VP1 : Virion. Host cytoplasm Reviewed prediction
Chain Protein 2B : Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Reviewed prediction
Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.
Chain Protein 2C : Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Reviewed prediction
Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. May associate with membranes through a N-terminal amphipathic helix By similarity.
Chain Protein 3A : Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Reviewed prediction
Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.
Chain Protein 3B : Virion Reviewed prediction
Chain Protease 3C : Host cytoplasm Reviewed prediction
Chain RNA-directed RNA polymerase 3D-POL : Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Reviewed prediction
Note: Interacts with membranes in a complex with viral protein 3AB. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 13771377Cytoplasmic Reviewed predictionAdd
BLAST
Intramembranei1378 – 139215 Reviewed predictionAdd
BLAST
Topological domaini1393 – 2134742Cytoplasmic Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. host cell cytoplasmic vesicle membrane Source: UniProtKB-SubCell
  2. integral to membrane of host cell Source: UniProtKB-KW
  3. membrane Source: UniProtKB-KW
  4. viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Host cytoplasmic vesicle, Host membrane, Membrane, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 21342134Genome polyproteinPRO_0000310495Add
BLAST
Chaini1 – 242242Protein VP0 Reviewed predictionPRO_0000310496Add
BLAST
Chaini1 – 1919Protein VP4 Reviewed predictionPRO_0000310497Add
BLAST
Chaini20 – 242223Protein VP2 Reviewed predictionPRO_0000310498Add
BLAST
Chaini243 – 487245Protein VP3 Reviewed predictionPRO_0000310499Add
BLAST
Chaini488 – 757270Protein VP1 Reviewed predictionPRO_0000310500Add
BLAST
Chaini758 – 80649Protein 2A Reviewed predictionPRO_0000310501Add
BLAST
Chaini807 – 1021215Protein 2B Reviewed predictionPRO_0000310502Add
BLAST
Chaini1022 – 1347326Protein 2C Reviewed predictionPRO_0000310503Add
BLAST
Chaini1348 – 141265Protein 3A Reviewed predictionPRO_0000310504Add
BLAST
Chaini1413 – 143321Protein 3B Reviewed predictionPRO_0000310505Add
BLAST
Chaini1434 – 1648215Protease 3C Reviewed predictionPRO_0000310506Add
BLAST
Chaini1649 – 2134486RNA-directed RNA polymerase 3D-POL Reviewed predictionPRO_0000310507Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1415 – 14151O-(5'-phospho-RNA)-tyrosine By similarity

Post-translational modificationi

Specific enzymatic cleavages by the viral protease in vivo yield a variety of precursors and mature proteins. During virion maturation, non-infectious particles are rendered infectious following cleavage of VP0. This maturation cleavage is followed by a conformational change of the particle By similarity.
VPg is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity.

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Proteomic databases

PRIDEiQ9YLS4.

Structurei

3D structure databases

ProteinModelPortaliQ9YLS4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1127 – 1289163SF3 helicaseAdd
BLAST
Domaini1433 – 1627195Peptidase C3Add
BLAST
Domaini1880 – 2001122RdRp catalyticAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi251 – 2544Poly-Ser

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 3 hits.
InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR007053. LRAT-like_dom.
IPR027417. P-loop_NTPase.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR001676. Picornavirus_capsid.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF04970. LRAT. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 2 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
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.

Q9YLS4-1 [UniParc]FASTAAdd to Basket

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MSKLFSTVGK TVDEVLSVLN DENTESYAGP DRTAVVGGGF LTTVDQSSVS     50
TATMGSLQDV QYRTAVDIPG SRVTQGERFF LIDQREWNST QSEWQLLGKI 100
DIVKELLDQS YAVDGLLKYH SYARFGLDVI VQINPTSFQA GGLIAALVPY 150
DQVDIESIAA MTTYCHGKLN CNINNVVRMK VPYIYSRGCY NLRNSAYSIW 200
MLVIRVWSQL QLGSGTSTQI TVTTLARFVD LELHGLSPLV AQMMRNEFRL 250
SSSSNIVNLA NYEDARAKVS LALGQEEFSR DSSSTGGELL HHFSQWTSIP 300
CLAFTFTFPG TVGPGTQIWS TTVDPFSCNL RASSTVHPTN LSSIAGMFCF 350
WRGDIVFEFQ VFCTKYHSGR LMFVYVPGDE NTKISTLTAK QASSGLTAVF 400
DINGVNSTLV FRCPFISDTP YRVNPTTHKS LWPYATGKLV CYVYNRLNAP 450
ASVSPSVSIN VYKSAVDLEL YAPVYGVSPT NTSVFAQGKE DEGGFSSVPE 500
VEQHVVEDKE PQGPLHVTPF GAVKAMEDPQ LARKTPGTFP ELAPGKPRHT 550
VDHMDLYKFM GRAHYLWGHK FTKTDMQYTF QIPLSPIKEG FVTGTLRWFL 600
SLFQLYRGSL DITMTFAGKT NVDGIVYFVP EGVAIETERE EQTPLLTLNY 650
KTSVGAIRFN TGQTTNVQFR IPFYTPLEHI ATHSKNAMDS VLGAITTQIT 700
NYSAQDEYLQ VTYYISFNED SQFSVPRAVP VVSSFTDTSS KTVMNTYWLD 750
DDELVEESSH SSFDEIEEAQ CSKCKMDLGD IVSCSGEKAK HFGVYVGDGV 800
VHVDPEGNAT NWFMKRKATV KKSKNLDKWC FALSPRIDRT LICETANLMV 850
GREVEYDIFV KNCETYARGI ASGDYGTKEG EKWKTLLSAV GVAAMTTTMM 900
AMRHELLDTS LTKLPQKVGE VTNEVRKILE DTSAGVREFK EKVSSILRKT 950
WPGKTSIKIM KWTCRIVKMC VGVGLCYAHG WDSKTVTAVV TMFSMDFLDL 1000
VIDGIEIGRM IIDELTTPKA QGLSEINQVL SIAKNAKDVI KMLIEIFCKV 1050
IERITGEHGK KIQWAQDKKE EIMNVLERAE KWITTSDDHS EGIECLKLVR 1100
SIQSVIRGEE SLKELAGELR AVGTHVLNKL GRLDKPNAPI LVRAEPTVLY 1150
LYGNRGGGKS LASMAIAVKL CKELGISHVE GIYTKPIMSD FWDGYAGQPV 1200
VIMDDLGQST SDEDWTNFCQ LVSSCPLRLN MANLEKKGTQ FNSPFIIASS 1250
NLSHPCPKTV YCTDAIARRL HIKVKVSPKE EFSTHAMLDV AKAKKAGAYC 1300
NLDCLDFQKI SDLASTPVSV QDIVLEMLHT NVDKQTLMGD IIQYWAQSNP 1350
REVFDTMAEG KNSGKYLWLF EKIKTSKWYI LGCVGAVLSV SVLGVFAYHM 1400
IKNHFRDQQH DQSAYSAAIK PLRVVRLEQS DAQSVVDISN VVHGNLVRVG 1450
VGPNEARIHW LYNGLGVYDT YILMPYHGIK DADVDDDLYI ERAGTIYSTN 1500
MKMVQVLFLE SREGDLVLIN VPRLPKFRDI RNHFSTEENI RRAEGMPGTL 1550
CTLDHERFTL VTESDLKMVE AATYVCEDDK GVRTDISVGR SWKAKACTVA 1600
GMCGGALVTS NNKMQNAIVG IHVAGGAHAI SRVITKEMIE EMLKTRAQCS 1650
RIWKTEFVEE KISVGSKTKY HKSPLYDFCP QEVIKCPTKL FYQGEIDVMQ 1700
VMLAKYSSPI VSEPLGYATV VEAYTNRMVS FFSEPRQLTY DECINGIEGL 1750
DAIDLKTSAG FPYNTLGLRK SDLIINGKMA QRLQQDVEKM EEDLHMNRSI 1800
QVVFTTCAKD ELRPLSKVML GKTRAIEACP VSFTILFRRY LGYALAQIQS 1850
HPGFHTGIAV GVDPDQDWHC MWYSIVTQCD LVVGLDFSNY DASLSPFMIY 1900
HAGRVLGQIC GLDPRLVDRI MEPIVNSVHQ LGSMRYYVHG SMPSGTPATS 1950
VLNSIINVVN ICHVLCALEK ISVFEVFKLF KILTYGDDVL LCIKKEYLDQ 2000
KSFPLSSFVQ GLEELGLSPT GADKMEVKVT PVHKMSFLKR TFYVDEWSIC 2050
HPRISEETVY SMLAWKSDNA SMKDLIETSI WFMFHHGPRK YVRFCTWLRG 2100
VLCRVGIGLY IPTYKELEVR YDRLVKYRFI DDSF 2134
Length:2,134
Mass (Da):238,980
Last modified:May 1, 1999 - v1
Checksum:i5BD829687E1ED30D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ225173 mRNA. Translation: CAA12416.1.
RefSeqiNP_653151.1. NC_003990.1.

Genome annotation databases

GeneIDi944582.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ225173 mRNA. Translation: CAA12416.1 .
RefSeqi NP_653151.1. NC_003990.1.

3D structure databases

ProteinModelPortali Q9YLS4.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi Q9YLS4.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 944582.

Family and domain databases

Gene3Di 2.60.120.20. 3 hits.
InterProi IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR007053. LRAT-like_dom.
IPR027417. P-loop_NTPase.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR001676. Picornavirus_capsid.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF04970. LRAT. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 2 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view ]
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. "Avian encephalomyelitis virus is a picornavirus and is most closely related to hepatitis A virus."
    Marvil P., Knowles N.J., Mockett A.P., Britton P., Brown T.D.K., Cavanagh D.
    J. Gen. Virol. 80:653-662(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].

Entry informationi

Entry nameiPOLG_AEVCA
AccessioniPrimary (citable) accession number: Q9YLS4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: May 1, 1999
Last modified: July 9, 2014
This is version 90 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

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