Q01206 (POL1_BAYMJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein 1 Cleaved into the following 8 chains: Protein P3 6 kDa protein 1 Short name=6K1 Cytoplasmic inclusion protein Short name=CI EC=3.6.4.- 6 kDa protein 2 Short name=6K2 Viral genome-linked protein Alternative name(s): VPg Nuclear inclusion protein A Short name=NI-a Short name=NIa EC=3.4.22.44 Alternative name(s): NIa-pro Nuclear inclusion protein B Short name=NI-b Short name=NIb EC=2.7.7.48 Alternative name(s): RNA-directed RNA polymerase Coat protein Short name=CP
Organism	Barley yellow mosaic virus (strain Japanese II-1) (BaYMV) [Complete proteome]
Taxonomic identifier	31729 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Bymovirus
Virus host	Hordeum vulgare (Barley) [TaxID: 4513]

Protein attributes

Sequence length	2410 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	Cytoplasmic inclusion protein has helicase activity. It may be involved in replication. Both 6K peptides are indispensable for virus replication By similarity. Nuclear inclusion protein A has proteolytic activity By similarity.
Catalytic activity	Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved. Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subcellular location	Coat protein: Virion Potential.
Post-translational modification	VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity. The viral RNA1 of bymoviruses is expressed as a single polyprotein which undergoes post-translational proteolytic processing by the main proteinase NIa-pro resulting in the production of at least eight individual proteins Potential.
Sequence similarities	Belongs to the bymoviruses polyprotein 1 family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 peptidase C4 domain. Contains 1 RdRp catalytic domain.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	Capsid protein Helicase Hydrolase Nucleotidyltransferase RNA-directed RNA polymerase Transferase
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 proteolysis Inferred from electronic annotation. Source: InterPro transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular component	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: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type peptidase activity Inferred from electronic annotation. Source: InterPro helicase activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 328	328	Protein P3 Potential		PRO_0000040546
	Chain	329 – 394	66	6 kDa protein 1 Potential		PRO_0000040547
	Chain	395 – 1053	659	Cytoplasmic inclusion protein Potential		PRO_0000040548
	Chain	1054 – 1175	122	6 kDa protein 2 Potential		PRO_0000040549
	Chain	1176 – 1338	163	Viral genome-linked protein Potential		PRO_0000040550
	Chain	1339 – 1586	248	Nuclear inclusion protein A Potential		PRO_0000040551
	Chain	1587 – 2113	527	Nuclear inclusion protein B Potential		PRO_0000040552
	Chain	2114 – 2410	297	Coat protein Potential		PRO_0000040553
Regions
	Domain	474 – 632	159	Helicase ATP-binding
	Domain	647 – 813	167	Helicase C-terminal
	Domain	1359 – 1573	215	Peptidase C4
	Domain	1857 – 1980	124	RdRp catalytic
	Nucleotide binding	487 – 494	8	ATP Potential
Sites
	Active site	1404	1	For nuclear inclusion protein A activity By similarity
	Active site	1440	1	For nuclear inclusion protein A activity By similarity
	Active site	1507	1	For nuclear inclusion protein A activity By similarity
	Site	328 – 329	2	Cleavage Potential
	Site	394 – 395	2	Cleavage Potential
	Site	1053 – 1054	2	Cleavage Potential
	Site	1175 – 1176	2	Cleavage Potential
	Site	1338 – 1339	2	Cleavage Potential
	Site	1586 – 1587	2	Cleavage Potential
	Site	2114 – 2115	2	Cleavage Potential
Amino acid modifications
	Modified residue	1234	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q01206 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: 6CFCF5D7045044B5	FASTA	2,410	270,770
	10 20 30 40 50 60 MEQTLAQAVS RKSKTDTPMA EERKHFSPMN FSANFVAPEL FYSANVRKIK NIFRERSTTR 70 80 90 100 110 120 FLDAISSDFE LVAFLTLSPA HLMQLETVLR HEMRSCVVPI VTSDASFETV AVIKTALDGM 130 140 150 160 170 180 RFHFGYTTLE KGWISMMRHA ESCLQESSSS AVNDLQTQIK RVGSLLLSGK NRVEGCELSV 190 200 210 220 230 240 LNLTARRFRI EYGLNGTYFG EHVAMLRGLK RYIYGTVPKE FLWAKTKKHS LFTIPAWIKR 250 260 270 280 290 300 TPIDCFLFCL RVIPILHRCG VAVSLIYWSC AAALNFPAFM SFLFKRQFAK YLAHSFAKHS 310 320 330 340 350 360 IYFMFLTIVA ILWSFRTFTS QKPKIVLQAR STAEKEKKLM MILASVVGIT YLFDYDIAEA 370 380 390 400 410 420 LGNCLHKISR LSSYLLDDHQ GIASRMFGAS YGLQAGDSAE DAVTTIISDL LSVTFKIVDE 430 440 450 460 470 480 DASQGTVEDA SETTFHSWVG VNTLAGRNMS RPLQYSVNET YALTPQNVQL QARKMADANN 490 500 510 520 530 540 CWSMVVGHTG SGKSTYLPVQ YSNYLSTKSD RRQQILICEP TQAATENVCA GVAANLGRAV 550 560 570 580 590 600 YGRHEGWSRM GDHCIQVMTY GSALQCHAMD PSFISTFDAI FLDEAHDVKE HSLVFESICD 610 620 630 640 650 660 TFKSVRKFYV SATPRDGSVC PEAARKYPLH VETSVCDSYR KFIAAQGGGD LLDISKHDTA 670 680 690 700 710 720 LVFLAGRPEC IKAANAWNAS VTGEKRAFSL SSDNFATDFS MLTERLKTHK TIIFTTNIIE 730 740 750 760 770 780 TGVTLSVDCV VDFGHTMRPC LDLNQKALRL DRRRVTRNER QQRIGRAGRL KDGYAIVCGD 790 800 810 820 830 840 VDRAVNVISP DVLYGAALLS FKHNVPFYMN ETFESSWLEG ITKAQADTMT IFKLPIFLTR 850 860 870 880 890 900 DLINADGSVA KEFLDVLKKH QFTTSDIKQA PSVTAKHIFP TWASYFSLHQ ALHYGDDKDE 910 920 930 940 950 960 VPHELRYARV PFSVTTLSKF DWPALALACE KHRASMSNVF AGIEEPARVV TLQTNPANIQ 970 980 990 1000 1010 1020 ASITHLTHMS KNYKTLIENN QHVRQSMVTN VMYKWFSSTR ITKDLDRNLR RCTDNLAVVE 1030 1040 1050 1060 1070 1080 ATLSSLRQIL AGNTQVHATP HMQSTLEDII GLQASDTLTE ESLASALGIF VPKSNLFLLL 1090 1100 1110 1120 1130 1140 ATKGFKLVYV VCILLLVNLV YLGLRKWREH LKQKGSNEIL TNTMPVSEGG EILAEVMKME 1150 1160 1170 1180 1190 1200 PKMRKNIKKD MDAAVESKLC GFTFVFPDDD KIGLEGKGNK YRPREDARLM YSTREDATLD 1210 1220 1230 1240 1250 1260 AWNEKAKERR KKVTDKSEPE LRRAYEKRPY FNFYDLQTDS NILEAIFYTT EGDEFFRTAD 1270 1280 1290 1300 1310 1320 PNKDMNLVAD KLRSFLDTKL VVGHHQRQML EETAKVVIKD TKGTAHHMDI SQHDPDHLKQ 1330 1340 1350 1360 1370 1380 NGSGKIGYPE HRGQFRQEGP AKTADYDLGV EFGTDTDDIT LEASTGILLS QVGVDVATRV 1390 1400 1410 1420 1430 1440 GRIFIGTFNM NCYFYSDWIL VPGHLQDRSG NVTIQFPDQT VQTTTDALNA NGVKRFYGLD 1450 1460 1470 1480 1490 1500 VIAIRRPAIL RPRTKLVKAF AIEEPVIAQM VFVDAQGVRK FTQSVRARKE ENSGRWSHKI 1510 1520 1530 1540 1550 1560 STVLGMCGCQ FWTLERQIDG IHVATNYTKK RNEFQPFTQE VVDFINGPGT KIPYCPWVFD 1570 1580 1590 1600 1610 1620 RPACGYASHT ALFEKPTTLT DIIHMQASDG LHNINNAIEG FGSSLRGQLV SPPTESTRQR 1630 1640 1650 1660 1670 1680 FDKLFGSGSF ELIGQMNKGL IDKHVIVGEN DDVHDFMREH PTFTWLKDFM NEYAPSVLSY 1690 1700 1710 1720 1730 1740 SAYYKDLCKY NRAKHVLTYN PEELHYATKG LIKMLEDAGL TQGSVRTPQQ VISDIQWNTS 1750 1760 1770 1780 1790 1800 AGPSYQGKKR DLCAHLSDDE VLHLAEVCRQ QFLEGKSTGV WNGSLKAELR TIEKVEAEKT 1810 1820 1830 1840 1850 1860 RVFTASPITS LFAMKFYVDD FNKKFYATNL KAPHTVGINK FGRGWEKLHD KLNRPGWLHG 1870 1880 1890 1900 1910 1920 SGDGSRFDSS IDPLFFDVVK TIRKHFLPSE HHKAIDLIYD EILNTTICLA NGMVIKKNVG 1930 1940 1950 1960 1970 1980 TQRQPSTVVD NTLVLMTAFL YAYIHKTGDR ELALLNERFI FVCNGDDNKF AISPQFDEEF 1990 2000 2010 2020 2030 2040 GHDFSPELVE LGLTYEFDDI TSDICENPYM SLTMVKTPFG VGFSLPVERI IAIMQWSKKG 2050 2060 2070 2080 2090 2100 GVLHSYLAGI SAIYESFNTP KLFKSIYAYL LWLTEEHEAE ILAAMTQSST ALPIPSMLDV 2110 2120 2130 2140 2150 2160 YRLHYGDDEI WLQAADPLTD AQKEDARIAA ADGARFELAD ADRRRKVEAD RVEAARVKKA 2170 2180 2190 2200 2210 2220 ADAALKPVNL TATRTPTEDD GKLKTPSGAR IPSSAADGNW SVPATKQVNA GLTLKIPLNK 2230 2240 2250 2260 2270 2280 LKSVPKSVME HNNSVALESE LKAWTDAVRT SLGITTDEAW IDALIPFIGW CCNNGTSDKH 2290 2300 2310 2320 2330 2340 AENQVMQIDS GKGAVTEMSL SPFIVHARMN GGLRRIMRNY SDETVLLITN NKLVAHWSMK 2350 2360 2370 2380 2390 2400 HGASANAKYA FDFFVPRSWM NPQDIEVSKQ ARLAALGTGT YNTMLTSDTT NLRKTTNHRV 2410 LDSDGHPELT

References

[1]	"Nucleotide sequence of barley yellow mosaic virus RNA 1: a close evolutionary relationship with potyviruses." Kashiwazaki S., Minobe Y., Omura T., Hibino H. J. Gen. Virol. 71:2781-2790(1990) [PubMed: 2273381] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Nucleotide sequence of the capsid protein gene of barley yellow mosaic virus." Kashiwazaki S., Hayano Y., Minobe Y., Omura T., Hibino H., Tsuchizaki T. J. Gen. Virol. 70:3015-3023(1989) [PubMed: 2584951] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	D01091 Genomic RNA. Translation: BAA00875.1.
PIR	JQ1948.
3D structure databases
ProteinModelPortal	Q01206.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR001650. Helicase_C. IPR009003. Pept_cys/ser_Trypsin-like. IPR001730. Peptidase_C4. IPR001592. Poty_coat. IPR013648. PP_Potyviridae. IPR001205. RNA-dir_pol_picornavirus. IPR007094. RNA-dir_pol_PSvirus. [Graphical view]
Pfam	PF00271. Helicase_C. 1 hit. PF00863. Peptidase_C4. 1 hit. PF00767. Poty_coat. 1 hit. PF08440. Poty_PP. 1 hit. PF00680. RdRP_1. 1 hit. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51436. POTYVIRUS_NIA_PRO. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POL1_BAYMJ

Accession

Primary (citable) accession number: Q01206

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1994
Last modified:	October 19, 2011
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program