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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).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).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).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).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).By similarity
RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals.PROSITE-ProRule annotation

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
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 – 202CleavageSequence Analysis
Sitei242 – 2432Cleavage; by protease 3CSequence Analysis
Sitei487 – 4882Cleavage; by protease 3CSequence Analysis
Sitei757 – 7582Cleavage; by hostSequence Analysis
Sitei806 – 8072Cleavage; by protease 3CBy similarity
Sitei1021 – 10222Cleavage; by protease 3CSequence Analysis
Sitei1347 – 13482Cleavage; by protease 3CSequence Analysis
Sitei1412 – 14132Cleavage; by protease 3CSequence Analysis
Sitei1433 – 14342Cleavage; by protease 3CSequence Analysis
Active sitei1477 – 14771For protease 3C activityBy similarity
Active sitei1515 – 15151For protease 3C activityBy similarity
Active sitei1603 – 16031For protease 3C activityBy similarity
Sitei1648 – 16492Cleavage; by protease 3CBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1153 – 11608ATPPROSITE-ProRule annotation

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 2B : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
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).By similarity
Chain Protein 2C : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
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).By similarity
Chain Protein 3A : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
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).By similarity
Chain RNA-directed RNA polymerase 3D-POL : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
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).By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 13771377CytoplasmicSequence AnalysisAdd
BLAST
Intramembranei1378 – 139215Sequence AnalysisAdd
BLAST
Topological domaini1393 – 2134742CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. host cell cytoplasmic vesicle Source: UniProtKB-KW
  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 VP0Sequence AnalysisPRO_0000310496Add
BLAST
Chaini1 – 1919Protein VP4Sequence AnalysisPRO_0000310497Add
BLAST
Chaini20 – 242223Protein VP2Sequence AnalysisPRO_0000310498Add
BLAST
Chaini243 – 487245Protein VP3Sequence AnalysisPRO_0000310499Add
BLAST
Chaini488 – 757270Protein VP1Sequence AnalysisPRO_0000310500Add
BLAST
Chaini758 – 80649Protein 2ASequence AnalysisPRO_0000310501Add
BLAST
Chaini807 – 1021215Protein 2BSequence AnalysisPRO_0000310502Add
BLAST
Chaini1022 – 1347326Protein 2CSequence AnalysisPRO_0000310503Add
BLAST
Chaini1348 – 141265Protein 3ASequence AnalysisPRO_0000310504Add
BLAST
Chaini1413 – 143321Protein 3BSequence AnalysisPRO_0000310505Add
BLAST
Chaini1434 – 1648215Protease 3CSequence AnalysisPRO_0000310506Add
BLAST
Chaini1649 – 2134486RNA-directed RNA polymerase 3D-POLSequence AnalysisPRO_0000310507Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Proteomic databases

PRIDEiQ9YLS4.

Structurei

3D structure databases

ProteinModelPortaliQ9YLS4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1127 – 1289163SF3 helicasePROSITE-ProRule annotationAdd
BLAST
Domaini1433 – 1627195Peptidase C3Add
BLAST
Domaini1880 – 2001122RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Compositional bias

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

Sequence similaritiesi

Belongs to the picornaviridae polyprotein family.Curated
Contains 1 peptidase C3 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

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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        10         20         30         40         50
MSKLFSTVGK TVDEVLSVLN DENTESYAGP DRTAVVGGGF LTTVDQSSVS
60 70 80 90 100
TATMGSLQDV QYRTAVDIPG SRVTQGERFF LIDQREWNST QSEWQLLGKI
110 120 130 140 150
DIVKELLDQS YAVDGLLKYH SYARFGLDVI VQINPTSFQA GGLIAALVPY
160 170 180 190 200
DQVDIESIAA MTTYCHGKLN CNINNVVRMK VPYIYSRGCY NLRNSAYSIW
210 220 230 240 250
MLVIRVWSQL QLGSGTSTQI TVTTLARFVD LELHGLSPLV AQMMRNEFRL
260 270 280 290 300
SSSSNIVNLA NYEDARAKVS LALGQEEFSR DSSSTGGELL HHFSQWTSIP
310 320 330 340 350
CLAFTFTFPG TVGPGTQIWS TTVDPFSCNL RASSTVHPTN LSSIAGMFCF
360 370 380 390 400
WRGDIVFEFQ VFCTKYHSGR LMFVYVPGDE NTKISTLTAK QASSGLTAVF
410 420 430 440 450
DINGVNSTLV FRCPFISDTP YRVNPTTHKS LWPYATGKLV CYVYNRLNAP
460 470 480 490 500
ASVSPSVSIN VYKSAVDLEL YAPVYGVSPT NTSVFAQGKE DEGGFSSVPE
510 520 530 540 550
VEQHVVEDKE PQGPLHVTPF GAVKAMEDPQ LARKTPGTFP ELAPGKPRHT
560 570 580 590 600
VDHMDLYKFM GRAHYLWGHK FTKTDMQYTF QIPLSPIKEG FVTGTLRWFL
610 620 630 640 650
SLFQLYRGSL DITMTFAGKT NVDGIVYFVP EGVAIETERE EQTPLLTLNY
660 670 680 690 700
KTSVGAIRFN TGQTTNVQFR IPFYTPLEHI ATHSKNAMDS VLGAITTQIT
710 720 730 740 750
NYSAQDEYLQ VTYYISFNED SQFSVPRAVP VVSSFTDTSS KTVMNTYWLD
760 770 780 790 800
DDELVEESSH SSFDEIEEAQ CSKCKMDLGD IVSCSGEKAK HFGVYVGDGV
810 820 830 840 850
VHVDPEGNAT NWFMKRKATV KKSKNLDKWC FALSPRIDRT LICETANLMV
860 870 880 890 900
GREVEYDIFV KNCETYARGI ASGDYGTKEG EKWKTLLSAV GVAAMTTTMM
910 920 930 940 950
AMRHELLDTS LTKLPQKVGE VTNEVRKILE DTSAGVREFK EKVSSILRKT
960 970 980 990 1000
WPGKTSIKIM KWTCRIVKMC VGVGLCYAHG WDSKTVTAVV TMFSMDFLDL
1010 1020 1030 1040 1050
VIDGIEIGRM IIDELTTPKA QGLSEINQVL SIAKNAKDVI KMLIEIFCKV
1060 1070 1080 1090 1100
IERITGEHGK KIQWAQDKKE EIMNVLERAE KWITTSDDHS EGIECLKLVR
1110 1120 1130 1140 1150
SIQSVIRGEE SLKELAGELR AVGTHVLNKL GRLDKPNAPI LVRAEPTVLY
1160 1170 1180 1190 1200
LYGNRGGGKS LASMAIAVKL CKELGISHVE GIYTKPIMSD FWDGYAGQPV
1210 1220 1230 1240 1250
VIMDDLGQST SDEDWTNFCQ LVSSCPLRLN MANLEKKGTQ FNSPFIIASS
1260 1270 1280 1290 1300
NLSHPCPKTV YCTDAIARRL HIKVKVSPKE EFSTHAMLDV AKAKKAGAYC
1310 1320 1330 1340 1350
NLDCLDFQKI SDLASTPVSV QDIVLEMLHT NVDKQTLMGD IIQYWAQSNP
1360 1370 1380 1390 1400
REVFDTMAEG KNSGKYLWLF EKIKTSKWYI LGCVGAVLSV SVLGVFAYHM
1410 1420 1430 1440 1450
IKNHFRDQQH DQSAYSAAIK PLRVVRLEQS DAQSVVDISN VVHGNLVRVG
1460 1470 1480 1490 1500
VGPNEARIHW LYNGLGVYDT YILMPYHGIK DADVDDDLYI ERAGTIYSTN
1510 1520 1530 1540 1550
MKMVQVLFLE SREGDLVLIN VPRLPKFRDI RNHFSTEENI RRAEGMPGTL
1560 1570 1580 1590 1600
CTLDHERFTL VTESDLKMVE AATYVCEDDK GVRTDISVGR SWKAKACTVA
1610 1620 1630 1640 1650
GMCGGALVTS NNKMQNAIVG IHVAGGAHAI SRVITKEMIE EMLKTRAQCS
1660 1670 1680 1690 1700
RIWKTEFVEE KISVGSKTKY HKSPLYDFCP QEVIKCPTKL FYQGEIDVMQ
1710 1720 1730 1740 1750
VMLAKYSSPI VSEPLGYATV VEAYTNRMVS FFSEPRQLTY DECINGIEGL
1760 1770 1780 1790 1800
DAIDLKTSAG FPYNTLGLRK SDLIINGKMA QRLQQDVEKM EEDLHMNRSI
1810 1820 1830 1840 1850
QVVFTTCAKD ELRPLSKVML GKTRAIEACP VSFTILFRRY LGYALAQIQS
1860 1870 1880 1890 1900
HPGFHTGIAV GVDPDQDWHC MWYSIVTQCD LVVGLDFSNY DASLSPFMIY
1910 1920 1930 1940 1950
HAGRVLGQIC GLDPRLVDRI MEPIVNSVHQ LGSMRYYVHG SMPSGTPATS
1960 1970 1980 1990 2000
VLNSIINVVN ICHVLCALEK ISVFEVFKLF KILTYGDDVL LCIKKEYLDQ
2010 2020 2030 2040 2050
KSFPLSSFVQ GLEELGLSPT GADKMEVKVT PVHKMSFLKR TFYVDEWSIC
2060 2070 2080 2090 2100
HPRISEETVY SMLAWKSDNA SMKDLIETSI WFMFHHGPRK YVRFCTWLRG
2110 2120 2130
VLCRVGIGLY IPTYKELEVR YDRLVKYRFI DDSF
Length:2,134
Mass (Da):238,980
Last modified:May 1, 1999 - v1
Checksum:i5BD829687E1ED30D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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: October 29, 2014
This is version 92 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