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Q9YLS4 (POLG_AEVCA) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 90. 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 12 chains:

  1. Protein VP0
    Alternative name(s):
    VP4-VP2
  2. Protein VP4
    Alternative name(s):
    P1A
    Virion protein 4
  3. Protein VP2
    Alternative name(s):
    P1B
    Virion protein 2
  4. Protein VP3
    Alternative name(s):
    P1C
    Virion protein 3
  5. Protein VP1
    Alternative name(s):
    P1D
    Virion protein 1
  6. Protein 2A
    Short name=P2A
  7. Protein 2B
    Short name=P2B
  8. Protein 2C
    Short name=P2C
    EC=3.6.1.15
  9. Protein 3A
    Short name=P3A
  10. Protein 3B
    Short name=P3B
    Alternative name(s):
    VPg
  11. Protease 3C
    Short name=P3C
    EC=3.4.22.28
    Alternative name(s):
    Picornain 3C
  12. RNA-directed RNA polymerase 3D-POL
    Short name=P3D-POL
    EC=2.7.7.48
OrganismAvian encephalomyelitis virus (strain Calnek vaccine) (AEV) [Reference proteome]
Taxonomic identifier475778 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeTremovirus
Virus hostAnas (ducks) [TaxID: 8835]
Gallus gallus (Chicken) [TaxID: 9031]
Phasianidae [TaxID: 9005]

Protein attributes

Sequence length2134 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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 activity

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.

Subcellular location

Protein VP2: Virion. Host cytoplasm Potential.

Protein VP3: Virion. Host cytoplasm Potential.

Protein VP1: Virion. Host cytoplasm Potential.

Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. 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.

Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. 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.

Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. 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.

Protein 3B: Virion Potential.

Protease 3C: Host cytoplasm Potential.

RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. 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.

Post-translational modification

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.

Sequence similarities

Belongs to the picornaviridae polyprotein family.

Contains 1 peptidase C3 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Ontologies

Keywords
   Biological processHost-virus interaction
Ion transport
Transport
Viral attachment to host cell
Viral RNA replication
Virus entry into host cell
   Cellular componentCapsid protein
Host cytoplasm
Host cytoplasmic vesicle
Host membrane
Membrane
Virion
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
Ion channel
Nucleotidyltransferase
Protease
RNA-directed RNA polymerase
Thiol protease
Transferase
Viral ion channel
   PTMCovalent protein-RNA linkage
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA-protein covalent cross-linking

Inferred from electronic annotation. Source: UniProtKB-KW

pore formation by virus in membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

protein oligomerization

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host RIG-I activity by RIG-I proteolysis

Inferred from sequence or structural similarity. Source: UniProtKB

transcription, DNA-templated

Inferred from electronic annotation. Source: InterPro

viral RNA genome replication

Inferred from electronic annotation. Source: InterPro

viral entry into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

virion attachment to host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componenthost cell cytoplasmic vesicle membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral to membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

membrane

Inferred from electronic annotation. Source: UniProtKB-KW

viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

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

ion channel activity

Inferred from electronic annotation. Source: UniProtKB-KW

structural molecule activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 21342134Genome polyprotein
PRO_0000310495
Chain1 – 242242Protein VP0 Potential
PRO_0000310496
Chain1 – 1919Protein VP4 Potential
PRO_0000310497
Chain20 – 242223Protein VP2 Potential
PRO_0000310498
Chain243 – 487245Protein VP3 Potential
PRO_0000310499
Chain488 – 757270Protein VP1 Potential
PRO_0000310500
Chain758 – 80649Protein 2A Potential
PRO_0000310501
Chain807 – 1021215Protein 2B Potential
PRO_0000310502
Chain1022 – 1347326Protein 2C Potential
PRO_0000310503
Chain1348 – 141265Protein 3A Potential
PRO_0000310504
Chain1413 – 143321Protein 3B Potential
PRO_0000310505
Chain1434 – 1648215Protease 3C Potential
PRO_0000310506
Chain1649 – 2134486RNA-directed RNA polymerase 3D-POL Potential
PRO_0000310507

Regions

Topological domain1 – 13771377Cytoplasmic Potential
Intramembrane1378 – 139215 Potential
Topological domain1393 – 2134742Cytoplasmic Potential
Domain1127 – 1289163SF3 helicase
Domain1433 – 1627195Peptidase C3
Domain1880 – 2001122RdRp catalytic
Nucleotide binding1153 – 11608ATP Potential
Compositional bias251 – 2544Poly-Ser

Sites

Active site14771For protease 3C activity By similarity
Active site15151For protease 3C activity By similarity
Active site16031For protease 3C activity By similarity
Site19 – 202Cleavage Potential
Site242 – 2432Cleavage; by protease 3C Potential
Site487 – 4882Cleavage; by protease 3C Potential
Site757 – 7582Cleavage; by host Potential
Site806 – 8072Cleavage; by protease 3C By similarity
Site1021 – 10222Cleavage; by protease 3C Potential
Site1347 – 13482Cleavage; by protease 3C Potential
Site1412 – 14132Cleavage; by protease 3C Potential
Site1433 – 14342Cleavage; by protease 3C Potential
Site1648 – 16492Cleavage; by protease 3C By similarity

Amino acid modifications

Modified residue14151O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q9YLS4 [UniParc].

Last modified May 1, 1999. Version 1.
Checksum: 5BD829687E1ED30D

FASTA2,134238,980
        10         20         30         40         50         60 
MSKLFSTVGK TVDEVLSVLN DENTESYAGP DRTAVVGGGF LTTVDQSSVS TATMGSLQDV 

        70         80         90        100        110        120 
QYRTAVDIPG SRVTQGERFF LIDQREWNST QSEWQLLGKI DIVKELLDQS YAVDGLLKYH 

       130        140        150        160        170        180 
SYARFGLDVI VQINPTSFQA GGLIAALVPY DQVDIESIAA MTTYCHGKLN CNINNVVRMK 

       190        200        210        220        230        240 
VPYIYSRGCY NLRNSAYSIW MLVIRVWSQL QLGSGTSTQI TVTTLARFVD LELHGLSPLV 

       250        260        270        280        290        300 
AQMMRNEFRL SSSSNIVNLA NYEDARAKVS LALGQEEFSR DSSSTGGELL HHFSQWTSIP 

       310        320        330        340        350        360 
CLAFTFTFPG TVGPGTQIWS TTVDPFSCNL RASSTVHPTN LSSIAGMFCF WRGDIVFEFQ 

       370        380        390        400        410        420 
VFCTKYHSGR LMFVYVPGDE NTKISTLTAK QASSGLTAVF DINGVNSTLV FRCPFISDTP 

       430        440        450        460        470        480 
YRVNPTTHKS LWPYATGKLV CYVYNRLNAP ASVSPSVSIN VYKSAVDLEL YAPVYGVSPT 

       490        500        510        520        530        540 
NTSVFAQGKE DEGGFSSVPE VEQHVVEDKE PQGPLHVTPF GAVKAMEDPQ LARKTPGTFP 

       550        560        570        580        590        600 
ELAPGKPRHT VDHMDLYKFM GRAHYLWGHK FTKTDMQYTF QIPLSPIKEG FVTGTLRWFL 

       610        620        630        640        650        660 
SLFQLYRGSL DITMTFAGKT NVDGIVYFVP EGVAIETERE EQTPLLTLNY KTSVGAIRFN 

       670        680        690        700        710        720 
TGQTTNVQFR IPFYTPLEHI ATHSKNAMDS VLGAITTQIT NYSAQDEYLQ VTYYISFNED 

       730        740        750        760        770        780 
SQFSVPRAVP VVSSFTDTSS KTVMNTYWLD DDELVEESSH SSFDEIEEAQ CSKCKMDLGD 

       790        800        810        820        830        840 
IVSCSGEKAK HFGVYVGDGV VHVDPEGNAT NWFMKRKATV KKSKNLDKWC FALSPRIDRT 

       850        860        870        880        890        900 
LICETANLMV GREVEYDIFV KNCETYARGI ASGDYGTKEG EKWKTLLSAV GVAAMTTTMM 

       910        920        930        940        950        960 
AMRHELLDTS LTKLPQKVGE VTNEVRKILE DTSAGVREFK EKVSSILRKT WPGKTSIKIM 

       970        980        990       1000       1010       1020 
KWTCRIVKMC VGVGLCYAHG WDSKTVTAVV TMFSMDFLDL VIDGIEIGRM IIDELTTPKA 

      1030       1040       1050       1060       1070       1080 
QGLSEINQVL SIAKNAKDVI KMLIEIFCKV IERITGEHGK KIQWAQDKKE EIMNVLERAE 

      1090       1100       1110       1120       1130       1140 
KWITTSDDHS EGIECLKLVR SIQSVIRGEE SLKELAGELR AVGTHVLNKL GRLDKPNAPI 

      1150       1160       1170       1180       1190       1200 
LVRAEPTVLY LYGNRGGGKS LASMAIAVKL CKELGISHVE GIYTKPIMSD FWDGYAGQPV 

      1210       1220       1230       1240       1250       1260 
VIMDDLGQST SDEDWTNFCQ LVSSCPLRLN MANLEKKGTQ FNSPFIIASS NLSHPCPKTV 

      1270       1280       1290       1300       1310       1320 
YCTDAIARRL HIKVKVSPKE EFSTHAMLDV AKAKKAGAYC NLDCLDFQKI SDLASTPVSV 

      1330       1340       1350       1360       1370       1380 
QDIVLEMLHT NVDKQTLMGD IIQYWAQSNP REVFDTMAEG KNSGKYLWLF EKIKTSKWYI 

      1390       1400       1410       1420       1430       1440 
LGCVGAVLSV SVLGVFAYHM IKNHFRDQQH DQSAYSAAIK PLRVVRLEQS DAQSVVDISN 

      1450       1460       1470       1480       1490       1500 
VVHGNLVRVG VGPNEARIHW LYNGLGVYDT YILMPYHGIK DADVDDDLYI ERAGTIYSTN 

      1510       1520       1530       1540       1550       1560 
MKMVQVLFLE SREGDLVLIN VPRLPKFRDI RNHFSTEENI RRAEGMPGTL CTLDHERFTL 

      1570       1580       1590       1600       1610       1620 
VTESDLKMVE AATYVCEDDK GVRTDISVGR SWKAKACTVA GMCGGALVTS NNKMQNAIVG 

      1630       1640       1650       1660       1670       1680 
IHVAGGAHAI SRVITKEMIE EMLKTRAQCS RIWKTEFVEE KISVGSKTKY HKSPLYDFCP 

      1690       1700       1710       1720       1730       1740 
QEVIKCPTKL FYQGEIDVMQ VMLAKYSSPI VSEPLGYATV VEAYTNRMVS FFSEPRQLTY 

      1750       1760       1770       1780       1790       1800 
DECINGIEGL DAIDLKTSAG FPYNTLGLRK SDLIINGKMA QRLQQDVEKM EEDLHMNRSI 

      1810       1820       1830       1840       1850       1860 
QVVFTTCAKD ELRPLSKVML GKTRAIEACP VSFTILFRRY LGYALAQIQS HPGFHTGIAV 

      1870       1880       1890       1900       1910       1920 
GVDPDQDWHC MWYSIVTQCD LVVGLDFSNY DASLSPFMIY HAGRVLGQIC GLDPRLVDRI 

      1930       1940       1950       1960       1970       1980 
MEPIVNSVHQ LGSMRYYVHG SMPSGTPATS VLNSIINVVN ICHVLCALEK ISVFEVFKLF 

      1990       2000       2010       2020       2030       2040 
KILTYGDDVL LCIKKEYLDQ KSFPLSSFVQ GLEELGLSPT GADKMEVKVT PVHKMSFLKR 

      2050       2060       2070       2080       2090       2100 
TFYVDEWSIC HPRISEETVY SMLAWKSDNA SMKDLIETSI WFMFHHGPRK YVRFCTWLRG 

      2110       2120       2130 
VLCRVGIGLY IPTYKELEVR YDRLVKYRFI DDSF 

« Hide

References

[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].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ225173 mRNA. Translation: CAA12416.1.
RefSeqNP_653151.1. NC_003990.1.

3D structure databases

ProteinModelPortalQ9YLS4.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEQ9YLS4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID944582.

Family and domain databases

Gene3D2.60.120.20. 3 hits.
InterProIPR000605. 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]
PfamPF04970. LRAT. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 2 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
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_AEVCA
AccessionPrimary (citable) accession number: Q9YLS4
Entry history
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 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