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Database: UniProt
Entry: Q9YJW3
LinkDB: Q9YJW3
Original site: Q9YJW3 
ID   POL1_BAYMY              Reviewed;        2410 AA.
AC   Q9YJW3;
DT   30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   11-DEC-2019, entry version 103.
DE   RecName: Full=Genome polyprotein 1;
DE   Contains:
DE     RecName: Full=Protein P3;
DE   Contains:
DE     RecName: Full=6 kDa protein 1;
DE              Short=6K1;
DE   Contains:
DE     RecName: Full=Cytoplasmic inclusion protein;
DE              Short=CI;
DE              EC=3.6.4.-;
DE   Contains:
DE     RecName: Full=6 kDa protein 2;
DE              Short=6K2;
DE   Contains:
DE     RecName: Full=Viral genome-linked protein;
DE     AltName: Full=VPg;
DE   Contains:
DE     RecName: Full=Nuclear inclusion protein A;
DE              Short=NI-a;
DE              Short=NIa;
DE              EC=3.4.22.44;
DE     AltName: Full=NIa-pro;
DE   Contains:
DE     RecName: Full=Nuclear inclusion protein B;
DE              Short=NI-b;
DE              Short=NIb;
DE              EC=2.7.7.48;
DE     AltName: Full=RNA-directed RNA polymerase;
DE   Contains:
DE     RecName: Full=Capsid protein;
DE              Short=CP;
DE     AltName: Full=Coat protein;
OS   Barley yellow mosaic virus (isolate China/Yancheng/1998) (BaYMV).
OC   Viruses; Riboviria; Potyviridae; Bymovirus.
OX   NCBI_TaxID=652104;
OH   NCBI_TaxID=4513; Hordeum vulgare (Barley).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=10500279; DOI=10.1016/s0168-1702(99)00076-3;
RA   Chen J., Shi N., Chen Y., Diao A., Chen D., Wilson M.A., Antoniw J.F.,
RA   Adams M.J.;
RT   "Molecular analysis of barley yellow mosaic virus isolates from China.";
RL   Virus Res. 64:13-21(1999).
CC   -!- FUNCTION: [Cytoplasmic inclusion protein]: has helicase activity. It
CC       may be involved in replication (By similarity). {ECO:0000250}.
CC   -!- FUNCTION: Both 6K peptides are indispensable for virus replication.
CC       {ECO:0000250}.
CC   -!- FUNCTION: [Nuclear inclusion protein A]: has proteolytic activity.
CC       {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Hydrolyzes glutaminyl bonds, and activity is further
CC         restricted by preferences for the amino acids in P6 - P1' that vary
CC         with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or
CC         Gly) for the enzyme from tobacco etch virus. The natural substrate is
CC         the viral polyprotein, but other proteins and oligopeptides
CC         containing the appropriate consensus sequence are also cleaved.;
CC         EC=3.4.22.44;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC         RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:11128, Rhea:RHEA-
CC         COMP:11129, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:83400;
CC         EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC   -!- SUBCELLULAR LOCATION: [Capsid protein]: Virion {ECO:0000305}.
CC   -!- PTM: VPg is uridylylated by the polymerase and is covalently attached
CC       to the 5'-end of the genomic RNA. This uridylylated form acts as a
CC       nucleotide-peptide primer for the polymerase (By similarity).
CC       {ECO:0000250}.
CC   -!- PTM: The viral RNA1 of bymoviruses is expressed as a single polyprotein
CC       which undergoes post-translational proteolytic processing by the main
CC       proteinase NIa-pro resulting in the production of at least eight
CC       individual proteins. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the bymoviruses polyprotein 1 family.
CC       {ECO:0000305}.
DR   EMBL; AJ132268; CAA10637.1; -; Genomic_RNA.
DR   RefSeq; NP_148999.1; NC_002990.1.
DR   PRIDE; Q9YJW3; -.
DR   GeneID; 963861; -.
DR   KEGG; vg:963861; -.
DR   Proteomes; UP000006704; Genome.
DR   GO; GO:0019029; C:helical viral capsid; IEA:UniProtKB-KW.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0008234; F:cysteine-type peptidase activity; IEA:InterPro.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR   GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
DR   GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR   GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR009003; Peptidase_S1_PA.
DR   InterPro; IPR001592; Poty_coat.
DR   InterPro; IPR001730; Potyv_NIa-pro_dom.
DR   InterPro; IPR013648; PP_Potyviridae.
DR   InterPro; IPR001205; RNA-dir_pol_C.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   Pfam; PF00863; Peptidase_C4; 1.
DR   Pfam; PF00767; Poty_coat; 1.
DR   Pfam; PF08440; Poty_PP; 1.
DR   Pfam; PF00680; RdRP_1; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SUPFAM; SSF50494; SSF50494; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
DR   PROSITE; PS51436; POTYVIRUS_NIA_PRO; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Capsid protein; Covalent protein-RNA linkage;
KW   Helical capsid protein; Helicase; Hydrolase; Nucleotide-binding;
KW   Nucleotidyltransferase; Phosphoprotein; Reference proteome;
KW   RNA-directed RNA polymerase; Transferase; Viral RNA replication; Virion.
FT   CHAIN           1..328
FT                   /note="Protein P3"
FT                   /id="PRO_5000064773"
FT   CHAIN           329..394
FT                   /note="6 kDa protein 1"
FT                   /id="PRO_5000064774"
FT   CHAIN           395..1053
FT                   /note="Cytoplasmic inclusion protein"
FT                   /id="PRO_5000064775"
FT   CHAIN           1054..1175
FT                   /note="6 kDa protein 2"
FT                   /id="PRO_5000064776"
FT   CHAIN           1176..1362
FT                   /note="Viral genome-linked protein"
FT                   /id="PRO_5000064777"
FT   CHAIN           1363..1586
FT                   /note="Nuclear inclusion protein A"
FT                   /id="PRO_5000064778"
FT   CHAIN           1587..2113
FT                   /note="Nuclear inclusion protein B"
FT                   /id="PRO_5000064779"
FT   CHAIN           2114..2410
FT                   /note="Capsid protein"
FT                   /id="PRO_5000064780"
FT   DOMAIN          474..632
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   DOMAIN          647..813
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT   DOMAIN          1359..1573
FT                   /note="Peptidase C4"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00766"
FT   DOMAIN          1857..1980
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   NP_BIND         487..494
FT                   /note="ATP"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   MOTIF           583..586
FT                   /note="DEAH box"
FT   COMPBIAS        147..150
FT                   /note="Poly-Ser"
FT   ACT_SITE        1404
FT                   /note="For nuclear inclusion protein A activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00766"
FT   ACT_SITE        1440
FT                   /note="For nuclear inclusion protein A activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00766"
FT   ACT_SITE        1507
FT                   /note="For nuclear inclusion protein A activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00766"
FT   SITE            328..329
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            394..395
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            1053..1054
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            1175..1176
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            1338..1339
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            1586..1587
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            2114..2115
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   MOD_RES         1234
FT                   /note="O-(5'-phospho-RNA)-tyrosine"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   2410 AA;  270904 MW;  277319D1E4CCA1F2 CRC64;
     MEQTLAQAVS RRNKTDTPMA EERKHFSPMN FSANFVAPEL FYSANVRKIK NIFKERSTTR
     FLDAISSDFE LVAFLTLSPA HLMQLETVLR QEMRSCAVPI VTSDASFETV AVIKTALDGM
     RFHFGYTTLE KGWISMMRHA ESCLQESSSS AVNDLQTPIK RVGSLLLSGK NRVEGCELSV
     LNLTARRFRI EYGLNGTYFG EHVAMLRDLK RYIYGTVPKE FLWAKTKKHL PFTIPAWITR
     TPIDCFLFCL RVIPILHRFG VAMSLIYFSC VAALNFPAFM GFLFKRQFAK YLAHSFAKHS
     IYFMFLTIVA ILWSFRTFTS QKPKIVLQAR STAEKEKKLM MILASVVGIT YLFDYDIAEA
     LGNCLHKISR LSSYLLDDHQ GIASRMFGAS YGLQAGDSAE DAVTTIISDL LSVTFKIVDE
     DASQGTVEDA SETTFHSWVG VNTLAGRNMS RPLQYSVNKT YALTPQNVQL QARAMADANN
     CWSMVVGHTG SGKSTYLPVQ YSNYLSTKSD RRQQILICEP TQAATENVCA GVAANLGRAV
     YGRHEGWSRM GDHCIQVMTY GSALQCHAMD PSFISTFDAI FLDEAHDVKE HSLVFESICD
     TFKSVRKFYV SATPRDGSVC PEAARKYPLH VETSVCDSYR KFIAAQGGGD LLDISKHDTA
     LVFLAGRPEC IKAANAWNAS VTGEKRAFSL SSDNFATDFS MLTERLKTHK TIIFTTNIIE
     TGVTLSVDCV VDFGHTMRPC LDLNQKSLRL DRRKVTRNER QQRIGPTGRL KDGYAIVCGD
     VDRAVNVISP DVLYGAALLS FKHNVPFYMN ETFESSWLKG VTKAQADTMT IFKLPIFLTR
     DLINADGSVA KEFLDVLKKH QFTTSDIKQA PSITAKHIFP TWASYFSLHQ ALHYGDDKDE
     IPHELRYARV PFSVTTLSKF DWPALALACE KHRASMSNVF AGIEEPARVV TLQTNPANIQ
     ASITHLMHMS KNYKTLIENN QHVRQSMMTN VMYKWFSSTR ITKDLDRNLR RCTDNLAVVE
     ATLSSLRQIL AGNTQVHATP HMQSTLEDII GLQASDTLTE ESLASALGIF VPKSNLFLLL
     ATKGFKLVYV ICILLLVNLV YIGLRKWREH LKQKGSDEIL TNTMPVSEGG EILAEVMKME
     PKMRKNIKRD MDEAVESKLC GFTFVFPDDD KIGLEGKGNK YRPREDARLM YSTREDATFD
     AWNEKAKERR KKVTDKSEPE LRRAYEKRPY FNFYDLQTDS NILEAIFYTT EGDEFFRTAD
     PNKDMNLVAD KLRSFLDTKL VVGHHQRKLL EETAQVVIKD TKGTAHKMEI SQHDPDCLKQ
     NGSGKVGYPE HRGQFRQEGV AITSDYDLGV EFGTDTDNIT LEASTGILLS QVGVDVATRV
     GRISIGTFNM NCYFYNDWIL VPGHLQDRSG NVTIQFPDQT VQTTTDALNA NGVKRFYGLD
     VIAIRRPAIL RPRTKLVKAF AIEEPVIAQM VFVDAQGVRK FTQSDWARKG ENSGRWSHKI
     STVLGMCGCQ FWTLERQIDG IHVATNYTKK RNEFQPFTQE VVDFINGPGT KIPYCPWVFD
     RPACGYASHT ALFEKPTTLT DVIHMQASDG LHNINNAIEG FGSSLRGQLV SPPTESTRQR
     FDKLFGSGSF ELIGQMNKGL IDKHVIVGEN DDVYDFMREH PTFTWLKDFM NEYAPSVLSY
     SAYYKDLCKY NRAKHVLTYN PEELHYATKG LIKMLEDAGL TQGSVRTPQQ VISDIQWNTS
     AGPSYQGKKR DLCAHLSDDE VLHLAEVCRQ QFLEGKSTGV WNGSLKAELR TIEKVEPEKT
     RVFTASPITS LFAMKFYVDD FNKKFYATNL KAPHTVGINK FGRGWERLHD KLNRPGWLHG
     SGDGSRFDSS IDPFFFDVVK TIRKHFLPSE HHKAIDLIYD EILNTTICLA NGMVIKKNVG
     TQRQPSTVVD NTLVLMTAFL YAYIHKTGDR ELALLNERFI FVCNGDDNKF AISPQFDEEF
     GHDFSPELVE LGLTYEFDDI TSDICENPYM SLTMVKTPFG VGFSLPVERI IAIMQWSKKG
     GVLHSYLAGI SAIYESFNTP KLFKSIYAYL LWLTEEHEAE ILAAMTQSST ALPIPSMLDV
     YRLHYGDDEI WLQAADPLTD AQKEAAHTAA ADRARLDLAD ADRRRKVEAD RVEAARVKKA
     ADAALKPVNL TATRMPTEDD GKLKTPSGAR IPSSAADGNW SVPATKQVNA GLTLKIPLNK
     LKSVPKSVME HNNSVALESE LKAWTDAVRT SLGITTDEAW IDALIPFIGW CCNNGTSDKH
     AENQVMQIDS GKGAVTEMSL SPFIVHARMN GGLRRIMRNY SDETVLLITN NKLVAHWSMK
     HGASANAKYA FDFFVPRSWM NPQDIEVSKQ ARLAALGTGT YNTMLTSDTT NLRKTTNHRV
     LDSDGHPELT
//
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