Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Genome polyprotein 1

Gene
N/A
Organism
Barley yellow mosaic virus (strain Japanese II-1) (BaYMV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

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 activityi

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).PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei1404 – 14041For nuclear inclusion protein A activityPROSITE-ProRule annotation
Active sitei1440 – 14401For nuclear inclusion protein A activityPROSITE-ProRule annotation
Active sitei1507 – 15071For nuclear inclusion protein A activityPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi487 – 4948ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nucleotidyltransferase, RNA-directed RNA polymerase, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein 1
Cleaved into the following 8 chains:
6 kDa protein 1
Short name:
6K1
6 kDa protein 2
Short name:
6K2
Alternative name(s):
VPg
Nuclear inclusion protein A (EC:3.4.22.44)
Short name:
NI-a
Short name:
NIa
Alternative name(s):
NIa-pro
Nuclear inclusion protein B (EC:2.7.7.48)
Short name:
NI-b
Short name:
NIb
Alternative name(s):
RNA-directed RNA polymerase
Coat protein
Short name:
CP
OrganismiBarley yellow mosaic virus (strain Japanese II-1) (BaYMV)
Taxonomic identifieri31729 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePotyviridaeBymovirus
Virus hostiHordeum vulgare (Barley) [TaxID: 4513]
Proteomesi
  • UP000007447 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Helical capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 328328Protein P3Sequence analysisPRO_0000040546Add
BLAST
Chaini329 – 394666 kDa protein 1Sequence analysisPRO_0000040547Add
BLAST
Chaini395 – 1053659Cytoplasmic inclusion proteinSequence analysisPRO_0000040548Add
BLAST
Chaini1054 – 11751226 kDa protein 2Sequence analysisPRO_0000040549Add
BLAST
Chaini1176 – 1338163Viral genome-linked proteinSequence analysisPRO_0000040550Add
BLAST
Chaini1339 – 1586248Nuclear inclusion protein ASequence analysisPRO_0000040551Add
BLAST
Chaini1587 – 2113527Nuclear inclusion protein BSequence analysisPRO_0000040552Add
BLAST
Chaini2114 – 2410297Coat proteinSequence analysisPRO_0000040553Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1234 – 12341O-(5'-phospho-RNA)-tyrosineBy similarity

Post-translational modificationi

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).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.Curated

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei328 – 3292CleavageSequence analysis
Sitei394 – 3952CleavageSequence analysis
Sitei1053 – 10542CleavageSequence analysis
Sitei1175 – 11762CleavageSequence analysis
Sitei1338 – 13392CleavageSequence analysis
Sitei1586 – 15872CleavageSequence analysis
Sitei2114 – 21152CleavageSequence analysis

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Proteomic databases

PRIDEiQ01206.

Structurei

3D structure databases

ProteinModelPortaliQ01206.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini474 – 632159Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini647 – 813167Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini1359 – 1573215Peptidase C4PROSITE-ProRule annotationAdd
BLAST
Domaini1857 – 1980124RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the bymoviruses polyprotein 1 family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 peptidase C4 domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR009003. Peptidase_S1_PA.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[Graphical view]
PfamiPF00863. Peptidase_C4. 1 hit.
PF00767. Poty_coat. 1 hit.
PF08440. Poty_PP. 1 hit.
PF00680. RdRP_1. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51192. 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]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q01206-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQTLAQAVS RKSKTDTPMA EERKHFSPMN FSANFVAPEL FYSANVRKIK
60 70 80 90 100
NIFRERSTTR FLDAISSDFE LVAFLTLSPA HLMQLETVLR HEMRSCVVPI
110 120 130 140 150
VTSDASFETV AVIKTALDGM RFHFGYTTLE KGWISMMRHA ESCLQESSSS
160 170 180 190 200
AVNDLQTQIK RVGSLLLSGK NRVEGCELSV LNLTARRFRI EYGLNGTYFG
210 220 230 240 250
EHVAMLRGLK RYIYGTVPKE FLWAKTKKHS LFTIPAWIKR TPIDCFLFCL
260 270 280 290 300
RVIPILHRCG VAVSLIYWSC AAALNFPAFM SFLFKRQFAK YLAHSFAKHS
310 320 330 340 350
IYFMFLTIVA ILWSFRTFTS QKPKIVLQAR STAEKEKKLM MILASVVGIT
360 370 380 390 400
YLFDYDIAEA LGNCLHKISR LSSYLLDDHQ GIASRMFGAS YGLQAGDSAE
410 420 430 440 450
DAVTTIISDL LSVTFKIVDE DASQGTVEDA SETTFHSWVG VNTLAGRNMS
460 470 480 490 500
RPLQYSVNET YALTPQNVQL QARKMADANN CWSMVVGHTG SGKSTYLPVQ
510 520 530 540 550
YSNYLSTKSD RRQQILICEP TQAATENVCA GVAANLGRAV YGRHEGWSRM
560 570 580 590 600
GDHCIQVMTY GSALQCHAMD PSFISTFDAI FLDEAHDVKE HSLVFESICD
610 620 630 640 650
TFKSVRKFYV SATPRDGSVC PEAARKYPLH VETSVCDSYR KFIAAQGGGD
660 670 680 690 700
LLDISKHDTA LVFLAGRPEC IKAANAWNAS VTGEKRAFSL SSDNFATDFS
710 720 730 740 750
MLTERLKTHK TIIFTTNIIE TGVTLSVDCV VDFGHTMRPC LDLNQKALRL
760 770 780 790 800
DRRRVTRNER QQRIGRAGRL KDGYAIVCGD VDRAVNVISP DVLYGAALLS
810 820 830 840 850
FKHNVPFYMN ETFESSWLEG ITKAQADTMT IFKLPIFLTR DLINADGSVA
860 870 880 890 900
KEFLDVLKKH QFTTSDIKQA PSVTAKHIFP TWASYFSLHQ ALHYGDDKDE
910 920 930 940 950
VPHELRYARV PFSVTTLSKF DWPALALACE KHRASMSNVF AGIEEPARVV
960 970 980 990 1000
TLQTNPANIQ ASITHLTHMS KNYKTLIENN QHVRQSMVTN VMYKWFSSTR
1010 1020 1030 1040 1050
ITKDLDRNLR RCTDNLAVVE ATLSSLRQIL AGNTQVHATP HMQSTLEDII
1060 1070 1080 1090 1100
GLQASDTLTE ESLASALGIF VPKSNLFLLL ATKGFKLVYV VCILLLVNLV
1110 1120 1130 1140 1150
YLGLRKWREH LKQKGSNEIL TNTMPVSEGG EILAEVMKME PKMRKNIKKD
1160 1170 1180 1190 1200
MDAAVESKLC GFTFVFPDDD KIGLEGKGNK YRPREDARLM YSTREDATLD
1210 1220 1230 1240 1250
AWNEKAKERR KKVTDKSEPE LRRAYEKRPY FNFYDLQTDS NILEAIFYTT
1260 1270 1280 1290 1300
EGDEFFRTAD PNKDMNLVAD KLRSFLDTKL VVGHHQRQML EETAKVVIKD
1310 1320 1330 1340 1350
TKGTAHHMDI SQHDPDHLKQ NGSGKIGYPE HRGQFRQEGP AKTADYDLGV
1360 1370 1380 1390 1400
EFGTDTDDIT LEASTGILLS QVGVDVATRV GRIFIGTFNM NCYFYSDWIL
1410 1420 1430 1440 1450
VPGHLQDRSG NVTIQFPDQT VQTTTDALNA NGVKRFYGLD VIAIRRPAIL
1460 1470 1480 1490 1500
RPRTKLVKAF AIEEPVIAQM VFVDAQGVRK FTQSVRARKE ENSGRWSHKI
1510 1520 1530 1540 1550
STVLGMCGCQ FWTLERQIDG IHVATNYTKK RNEFQPFTQE VVDFINGPGT
1560 1570 1580 1590 1600
KIPYCPWVFD RPACGYASHT ALFEKPTTLT DIIHMQASDG LHNINNAIEG
1610 1620 1630 1640 1650
FGSSLRGQLV SPPTESTRQR FDKLFGSGSF ELIGQMNKGL IDKHVIVGEN
1660 1670 1680 1690 1700
DDVHDFMREH PTFTWLKDFM NEYAPSVLSY SAYYKDLCKY NRAKHVLTYN
1710 1720 1730 1740 1750
PEELHYATKG LIKMLEDAGL TQGSVRTPQQ VISDIQWNTS AGPSYQGKKR
1760 1770 1780 1790 1800
DLCAHLSDDE VLHLAEVCRQ QFLEGKSTGV WNGSLKAELR TIEKVEAEKT
1810 1820 1830 1840 1850
RVFTASPITS LFAMKFYVDD FNKKFYATNL KAPHTVGINK FGRGWEKLHD
1860 1870 1880 1890 1900
KLNRPGWLHG SGDGSRFDSS IDPLFFDVVK TIRKHFLPSE HHKAIDLIYD
1910 1920 1930 1940 1950
EILNTTICLA NGMVIKKNVG TQRQPSTVVD NTLVLMTAFL YAYIHKTGDR
1960 1970 1980 1990 2000
ELALLNERFI FVCNGDDNKF AISPQFDEEF GHDFSPELVE LGLTYEFDDI
2010 2020 2030 2040 2050
TSDICENPYM SLTMVKTPFG VGFSLPVERI IAIMQWSKKG GVLHSYLAGI
2060 2070 2080 2090 2100
SAIYESFNTP KLFKSIYAYL LWLTEEHEAE ILAAMTQSST ALPIPSMLDV
2110 2120 2130 2140 2150
YRLHYGDDEI WLQAADPLTD AQKEDARIAA ADGARFELAD ADRRRKVEAD
2160 2170 2180 2190 2200
RVEAARVKKA ADAALKPVNL TATRTPTEDD GKLKTPSGAR IPSSAADGNW
2210 2220 2230 2240 2250
SVPATKQVNA GLTLKIPLNK LKSVPKSVME HNNSVALESE LKAWTDAVRT
2260 2270 2280 2290 2300
SLGITTDEAW IDALIPFIGW CCNNGTSDKH AENQVMQIDS GKGAVTEMSL
2310 2320 2330 2340 2350
SPFIVHARMN GGLRRIMRNY SDETVLLITN NKLVAHWSMK HGASANAKYA
2360 2370 2380 2390 2400
FDFFVPRSWM NPQDIEVSKQ ARLAALGTGT YNTMLTSDTT NLRKTTNHRV
2410
LDSDGHPELT
Length:2,410
Mass (Da):270,770
Last modified:February 1, 1994 - v1
Checksum:i6CFCF5D7045044B5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D01091 Genomic RNA. Translation: BAA00875.1.
PIRiJQ1948.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D01091 Genomic RNA. Translation: BAA00875.1.
PIRiJQ1948.

3D structure databases

ProteinModelPortaliQ01206.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ01206.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR009003. Peptidase_S1_PA.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[Graphical view]
PfamiPF00863. Peptidase_C4. 1 hit.
PF00767. Poty_coat. 1 hit.
PF08440. Poty_PP. 1 hit.
PF00680. RdRP_1. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51192. 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]
ProtoNetiSearch...

Publicationsi

  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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiPOL1_BAYMJ
AccessioniPrimary (citable) accession number: Q01206
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: May 11, 2016
This is version 111 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

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.