Q6WQ42 (POLG_AEVL2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 12 chains: Protein VP0 Alternative name(s): VP4-VP2 Protein VP4 Alternative name(s): P1A Virion protein 4 Protein VP2 Alternative name(s): P1B Virion protein 2 Protein VP3 Alternative name(s): P1C Virion protein 3 Protein VP1 Alternative name(s): P1D Virion protein 1 Protein 2A Short name=P2A Protein 2B Short name=P2B Protein 2C Short name=P2C EC=3.6.1.15 Protein 3A Short name=P3A Protein 3B Short name=P3B Alternative name(s): VPg Picornain 3C EC=3.4.22.28 Alternative name(s): Protease 3C Short name=P3C RNA-directed RNA polymerase 3D-POL Short name=P3D-POL EC=2.7.7.48
Organism	Avian encephalomyelitis virus (strain L2Z) (AEV) [Complete proteome]
Taxonomic identifier	475780 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Picornaviridae › Tremovirus › Avian encephalomyelitis virus
Virus host	Anas (ducks) [TaxID: 8835] Gallus gallus (Chicken) [TaxID: 9031] Phasianidae [TaxID: 9005]

Protein attributes

Sequence length	2134 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

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. 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. Protein 3C is a 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 co-operatively 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. Picornain 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 process	Host-virus interaction Ion transport Transport Viral RNA replication Viral attachment to host cell Virus entry into host cell
Cellular component	Host cytoplasm Host cytoplasmic vesicle Host membrane Membrane Virion
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Capsid protein Helicase Hydrolase Ion channel Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase Viral ion channel
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW ion transport Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral attachment to host cell Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell Inferred from electronic annotation. Source: UniProtKB-KW viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell cytoplasmic vesicle membrane Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP 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 structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 2134	2134	Genome polyprotein By similarity		PRO_0000310521
	Chain	1 – 242	242	Protein VP0 Potential		PRO_0000310522
	Chain	1 – 19	19	Protein VP4 Potential		PRO_0000310523
	Chain	20 – 242	223	Protein VP2 Potential		PRO_0000310524
	Chain	243 – 487	245	Protein VP3 Potential		PRO_0000310525
	Chain	488 – 757	270	Protein VP1 Potential		PRO_0000310526
	Chain	758 – 806	49	Protein 2A Potential		PRO_0000310527
	Chain	807 – 1021	215	Protein 2B Potential		PRO_0000310528
	Chain	1022 – 1347	326	Protein 2C Potential		PRO_0000310529
	Chain	1348 – 1412	65	Protein 3A Potential		PRO_0000310530
	Chain	1413 – 1433	21	Protein 3B Potential		PRO_0000310531
	Chain	1434 – 1648	215	Picornain 3C Potential		PRO_0000310532
	Chain	1649 – 2134	486	RNA-directed RNA polymerase 3D-POL Potential		PRO_0000310533
Regions
	Topological domain	1 – 1377	1377	Cytoplasmic Potential
	Intramembrane	1378 – 1392	15	Potential
	Topological domain	1393 – 2134	742	Cytoplasmic Potential
	Domain	1127 – 1289	163	SF3 helicase
	Domain	1433 – 1627	195	Peptidase C3
	Domain	1880 – 2001	122	RdRp catalytic
	Nucleotide binding	1153 – 1160	8	ATP Potential
	Compositional bias	251 – 254	4	Poly-Ser
Sites
	Active site	1477	1	For picornain 3C activity By similarity
	Active site	1515	1	For picornain 3C activity By similarity
	Active site	1603	1	For picornain 3C activity By similarity
	Site	19 – 20	2	Cleavage Potential
	Site	242 – 243	2	Cleavage; by picornain 3C Potential
	Site	487 – 488	2	Cleavage; by picornain 3C Potential
	Site	757 – 758	2	Cleavage; by host Potential
	Site	806 – 807	2	Cleavage; by picornain 3C By similarity
	Site	1021 – 1022	2	Cleavage; by picornain 3C Potential
	Site	1347 – 1348	2	Cleavage; by picornain 3C Potential
	Site	1412 – 1413	2	Cleavage; by picornain 3C Potential
	Site	1433 – 1434	2	Cleavage; by picornain 3C Potential
	Site	1648 – 1649	2	Cleavage; by picornain 3C By similarity
Amino acid modifications
	Modified residue	1415	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q6WQ42 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: C194284F02131E6B	FASTA	2,134	238,653
	10 20 30 40 50 60 MSKLFSTVGR TVDEVLSVLN DEDTESYAGP DRTAVVGGGF LTTVDQSSVS TATMGSLQDV 70 80 90 100 110 120 QYRTAVDIPG SRVTQGERFF LIDQREWNST QSEWQLLGKI DIVKELLDQS YAVDGLLKYH 130 140 150 160 170 180 SYARFGLDVI VQINPTSFQA GGLIAALVPY DQVDIESIVA MTTYCHGKVN CNINYVVRMK 190 200 210 220 230 240 VPYIYSRGCY NLRNSAYSIW MLVIRVWSRL QLGSGTSTQI TITTLARFVD LELHGLSPLV 250 260 270 280 290 300 AQMMRNEFRL SSSSNIVNLA NYDDARAKVS LALGQEEFSR DSSSTGGELV HHFSQWTSIP 310 320 330 340 350 360 CLAFTFTFPG TVGPGTHIWS TTVDPFSCNL RASSTVHPTN LSSIAGMFCF WRGDIVFEFQ 370 380 390 400 410 420 VFCTKYHSGR LMFVYVPGDE NTKISTLTAK QASTGLTAVF DINGVNSTLV FRCPFISDTP 430 440 450 460 470 480 YRVNPTTHKS LWPYATGKLV CYVYNILNAP ASVSPSVSIN VYKSAADLEL YAPVYGVSPT 490 500 510 520 530 540 NTSIFAQGKE DEGGFFSVPE VEQHVVEDKE PQGPLHVTPF GAVKAMEDPQ LARKTPGTFP 550 560 570 580 590 600 ELAPGKPRHT VDHMDLYKFM GRAHYLWGHE 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 IVICSGEKAK HFGVYVGDGV VHVDPEGNAT NWFMKRKATV KKSKNLDKWC FALSPRIDRT 850 860 870 880 890 900 LICETANLMV GREVEYDIFV KNCETYARGI ASGDYGTKEG EKWKTLLSAV GVAAMTTTMM 910 920 930 940 950 960 AMRHQLLDTS LTKLPQKVGE VTNEVRKILE DTSAGVREFK EKVSSILRKT WPGKTSIKIM 970 980 990 1000 1010 1020 KWTFRIVKMC VGVGLCYAHG WDSKPVTAVV TMFSMDFLDL VIDGIEIGRM IIHELTTPKA 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 QDIVLALLHT NVDKQTVMGN IIQYWAQSNP REVFDTMAEG KNSGKYLWLF EKIKTSKWYI 1390 1400 1410 1420 1430 1440 LGCVGAALSV SVLGVFAYHM IKNHFRDQQH DQSAYSAAIK PLRVVRLEQS DAQSVVDISN 1450 1460 1470 1480 1490 1500 VVHGNLVRVG VGPNEARIHW LNNGWGVYNT 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 IHVAGGAPAI SRVITKEMIE EMLKTRAQCS RIWKTEFVEK KISVGSKTKY HKSPLYDFCP 1690 1700 1710 1720 1730 1740 QKVIKCPTKL FYQGEIDVMQ VMLAKYSSPI VSEPLGYATV VEAYTNRMVS FFSEPRQLTY 1750 1760 1770 1780 1790 1800 DECINGIEGL DAIDLKTSAG FPYNTLSLKK SDLIINGKKA QRLQQDVEKM EEDLHMNRSI 1810 1820 1830 1840 1850 1860 QVVFTTCAKD ELRPLSKGML GKTRAIKACP VSFTILFRKY LGYALAQIQS HPGFHTGIAV 1870 1880 1890 1900 1910 1920 GVDPDQDWHC MWYSIVTQCD LVVGLDFSNY DASLSPFMIY HAGRVLGQIC GLDPRLVDRI 1930 1940 1950 1960 1970 1980 MEPIVNSVHQ LGSMRYYVDG SMPSGTPATS VLNSIINVVN ISHVLCALEK ISVFEVFKLS 1990 2000 2010 2020 2030 2040 KILTYGDDVL FCIKKESLDQ KSFPLSSFVQ GLKELGMSPT GADKMEVKVT PVHKMSFLKR 2050 2060 2070 2080 2090 2100 TFYVDEWSIC HPRISEETVY SMLAWKSDNA SMKHVIETSI WFMFHHGPRK YVIFCTCLRG 2110 2120 2130 VLCRVGIGLY IPTYKELEVR YDRLVKDRVI DDSF

References

[1]	"Determination of the whole genome of avian encephalomyelitis virus isolate from China." Wei L., Liu J., Yao W. Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY275539 Genomic RNA. Translation: AAN09930.2.
3D structure databases
HSSP	HSSP built from PDB template 1HAV based on UniProtKB P08617.
ProteinModelPortal	Q6WQ42.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR014759. Helicase_SF3_ssRNA_vir. IPR007053. LRAT-like_dom. IPR000199. Peptidase_C3A/C3B_picornavir. IPR001676. Picornavirus_capsid. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. IPR009003. Trypsin-like_Pept_dom. [Graphical view]
Pfam	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]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	PS50507. RDRP_SSRNA_POS. 1 hit. PS51218. SF3_HELICASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_AEVL2

Accession

Primary (citable) accession number: Q6WQ42

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 13, 2007
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program