POL1_BAYMY
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 03-AUG-2022, entry version 110.
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; Orthornavirae; Pisuviricota; Stelpaviricetes;
OC Patatavirales; 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: [6 kDa protein 1]: Indispensable for virus replication.
CC {ECO:0000250|UniProtKB:P13529}.
CC -!- FUNCTION: [6 kDa protein 2]: Indispensable for virus replication.
CC {ECO:0000250|UniProtKB:P09814}.
CC -!- FUNCTION: [Viral genome-linked protein]: Mediates the cap-independent,
CC EIF4E-dependent translation of viral genomic RNAs (By similarity).
CC Binds to the cap-binding site of host EIF4E and thus interferes with
CC the host EIF4E-dependent mRNA export and translation (By similarity).
CC VPg-RNA directly binds EIF4E and is a template for transcription (By
CC similarity). Also forms trimeric complexes with EIF4E-EIF4G, which are
CC templates for translation (By similarity).
CC {ECO:0000250|UniProtKB:P18247}.
CC -!- FUNCTION: [Nuclear inclusion protein A]: Has RNA-binding and
CC proteolytic activities. {ECO:0000250|UniProtKB:P04517}.
CC -!- FUNCTION: [Nuclear inclusion protein B]: An RNA-dependent RNA
CC polymerase that plays an essential role in the virus replication.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
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; Evidence={ECO:0000250|UniProtKB:P04517};
CC -!- SUBCELLULAR LOCATION: [6 kDa protein 1]: Host cytoplasmic vesicle.
CC Note=Probably colocalizes with 6K2-induced vesicles associated with
CC host chloroplasts. {ECO:0000250|UniProtKB:P13529}.
CC -!- SUBCELLULAR LOCATION: [6 kDa protein 2]: Host cytoplasmic vesicle
CC {ECO:0000250|UniProtKB:P09814}. Note=6K-induced vesicles associate with
CC host chloroplasts. {ECO:0000250|UniProtKB:P09814}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein]: Virion {ECO:0000305}.
CC -!- PTM: [Viral genome-linked protein]: VPg is uridylylated by the
CC polymerase and is covalently attached to the 5'-end of the genomic RNA.
CC This uridylylated form acts as a nucleotide-peptide primer for the
CC polymerase (By similarity). {ECO:0000250|UniProtKB:P09814}.
CC -!- PTM: [Genome polyprotein 1]: The viral RNA1 of bymoviruses is expressed
CC as a single polyprotein which undergoes post-translational proteolytic
CC processing by the main proteinase NIa-pro resulting in the production
CC of at least eight individual proteins. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the bymoviruses polyprotein 1 family.
CC {ECO:0000305}.
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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:0016818; F:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; IEA:InterPro.
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:0006508; P:proteolysis; 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 Gene3D; 2.40.10.10; -; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR009003; Peptidase_S1_PA.
DR InterPro; IPR043504; Peptidase_S1_PA_chymotrypsin.
DR InterPro; IPR001592; Poty_coat.
DR InterPro; IPR001730; Potyv_NIa-pro_dom.
DR InterPro; IPR013648; PP_Potyviridae.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
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 SUPFAM; SSF56672; SSF56672; 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; Host cytoplasmic vesicle; Hydrolase;
KW Nucleotide-binding; Nucleotidyltransferase; Phosphoprotein;
KW Reference proteome; RNA-directed RNA polymerase; Transferase;
KW Viral RNA replication; Virion.
FT CHAIN 1..2410
FT /note="Genome polyprotein 1"
FT /id="PRO_0000456245"
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 REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2175..2200
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 583..586
FT /note="DEAH box"
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 BINDING 487..494
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
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|UniProtKB:P09814"
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
