POL1_BAYMG
ID POL1_BAYMG Reviewed; 2412 AA.
AC Q04574;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 128.
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=Coat protein;
DE Short=CP;
OS Barley yellow mosaic virus (isolate Germany) (BaYMV).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Stelpaviricetes;
OC Patatavirales; Potyviridae; Bymovirus.
OX NCBI_TaxID=31728;
OH NCBI_TaxID=4513; Hordeum vulgare (Barley).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=1588327; DOI=10.1099/0022-1317-73-5-1303;
RA Peerenboom E., Proels M., Schell J., Steinbiss H.-H., Davidson A.D.;
RT "The complete nucleotide sequence of RNA 1 of a German isolate of barley
RT yellow mosaic virus and its comparison with a Japanese isolate.";
RL J. Gen. Virol. 73:1303-1308(1992).
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: [Coat 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; X69757; CAA49412.1; -; Genomic_RNA.
DR PIR; JQ1537; JQ1537.
DR Proteomes; UP000007446; 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; IPR001650; Helicase_C.
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 PRINTS; PR00966; NIAPOTYPTASE.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF50494; SSF50494; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
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 RNA-directed RNA polymerase; Transferase; Viral RNA replication; Virion.
FT CHAIN 1..2412
FT /note="Genome polyprotein 1"
FT /id="PRO_0000456243"
FT CHAIN 1..328
FT /note="Protein P3"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040538"
FT CHAIN 329..394
FT /note="6 kDa protein 1"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040539"
FT CHAIN 395..1053
FT /note="Cytoplasmic inclusion protein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040540"
FT CHAIN 1054..1175
FT /note="6 kDa protein 2"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040541"
FT CHAIN 1176..1338
FT /note="Viral genome-linked protein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040542"
FT CHAIN 1339..1587
FT /note="Nuclear inclusion protein A"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040543"
FT CHAIN 1588..2115
FT /note="Nuclear inclusion protein B"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040544"
FT CHAIN 2116..2412
FT /note="Coat protein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000040545"
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..1574
FT /note="Peptidase C4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00766"
FT DOMAIN 1858..1982
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2178..2202
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
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 1587..1588
FT /note="Cleavage"
FT /evidence="ECO:0000255"
FT SITE 2115..2116
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 2412 AA; 270876 MW; 439597DB4B4313AF CRC64;
MEQTLAQAVS RRGKTNTPMA EERKPFSPMN FSANFVAPEL FYSANVRKIK NIFRERSTTR
FLDAISSDFE LVAFLTLSPA HLMQLETTLR QEIRSCVVPI VTSDASFETV AVIKTALDGM
RFHFGHTTLE KGWMSMMRHA ESCLQESSSS AVNDLQMQIK RVGSLLLSGK NRVESCELSV
LNLTARRFRI EYGLNGTYFG EHVAMLLDLK RYIYGTVPKE FCWAKTKKHS LFTTPKWIKR
TPIDCFLFCL RVIPILHRFG VAISLLYWSC VAALNFPAFM AFLFKRQFAK YLAHSFAKHS
IYFIFLTIIA ILWSFRTFAS QKPKIVLQAR STAEKEKKLM MILASVVGIT YLFDYDIAEA
LGNCLHKISR LSSYLLDDHQ GIASRMFGAS YGLQAGDSAE DAVTTIISDL LSVTFKIVDE
DASQGTVEDA SETTFHSWVG VNTLAGRNMS RPLQYDVNKT YALTPQNVQL QARAMADANN
CWSMVVGHTG SGKSTYLPVQ YSNYLSTKSD RRQQILICEP TQAATENVCA GVAANLGRAV
YGRHEGWSRM GDHCIQVMTY GSALQCHAMD PSFISTFDAI FLDEAHDVKE HSLVFESICD
TFKSVRKFYV SATPRDGSVC PEAARKYPLH VETSVCDSYR KFIAAQGGGD LLDISKHDTA
LVFLAGRPEC IKAANAWNAS VTGEKRAFPL SSDNFATDFS MLTERLKTHK TIIFTTNIIE
TGVTLSVDCV VDFGHTMRPC LDLNQKSLRL DRRRVTRNER QQRIGRAGRL KDGYAIVCGD
VDRAVNVISP DVLYGAALLS FKHNVPFYMN ETFESSWLEG VTKAQADTMT IFKLPIFLTR
DLINADGSVA REFLDVLKKH QFTTSDIKQA PSVTAKHIFP TWASYFSLHQ ALHYGDDKDE
IPHELRYARV PFSVTTLSKF DWPALALACE KHRASMSNVF AGIEEPARVV TLQTNPANIQ
ASITHLTHMS KNYKTLIENN QHVRQSMMTN VMFKWFSSTR ITKDLDRNLR RCTDNLSVVE
ATLSSLRQIL AGNTQVHATP HMQSTLEDII ELQASDTLTE ESLANALGIF VPKCNLFLLL
ATKGFKLVYV VCILLLVNLV YTGLRKWREH LKQKGSNEIL TNTMPVSEGG EILAEVMKME
PKMRKNIKRD MDAAVESKLC GFTFVFPDDD KIGLEGKGNK YRPREDARLM YSTREDATFD
AWNEKAKERR KKVTDKAEPE LRRAYEKRPY FNFYDLQTDS NILEAIFYTT EGDEFFRTAD
PNRDMNLVAD KLRSFLDTKL VVGHHQRKLL EETANVVIKD TKGTAHKMEI SQHDPDFLKQ
NGSGKVGYPE HRGQFRQEGV AVTGDYDLEA EFGTDTDEIS FGASTGILLS QVGVDVATRV
GRICIGTFNM NCYFYSDWIL VPGHLQDRSG NVTIQFPDQT VQTTTDALNA NGVKRFYGLD
VIAIRRPAIL RPRTKLVKAF AIEEPVIAQM VFVDAQGVRK FTQSDWARKE ENSGRWSHKI
STVLGMCGCP VLDVGKNRLI GIHVATNYTK KRNEFQPFTQ EVVDFINGPG TKIPYCPWVF
DRPACGYSSH NALFEKPTTL ADVIHMQASD GLHNINNAIE GFGSSLKGQL VSPPTESTRQ
RFDKLFGSGS FELIGQMNKG LIDKHVIVGE NDDVYDFMRE HPTFTWLKDF MNEYAPSVLS
YSAYYKDLCK YNRAKHVLTY NPEELHCATK GLIKMLEDAG LTQGSVRTPQ QVVSDIQWNT
SAGPSYQGKK RDLCAHLSDD EVLHLAEVCR QQFLEGKSTG VWNGSLKAEL RTIEKVEAEK
TRVFTASPIT SLFAMKFYVD DFNKKFYATN LKAPHTVGIN KFGRGWEKLH DKLNRPGWLH
GSGDGSRFDS SIDPFFFDVV KTIRKHFLPS EHHKAIDLIY DEILNTTICL ANGMVIRKNV
GNNSGQPSTV VDNTLVLMTA FLYAYIHKTG DRELALLNER FIFVCNGDDN KFAISPQFDE
EFGHDFSPEL VELGLTYEFD DITSDICENP YMSLTMVKTP FGVGFSLPVE RIIAIMQWSK
KGGVLHSYLA GISAIYESFN TPKLFKSIYA YLLWLTEEHE AEILAAMTQS STALPIPSML
DVYRLHYGDD EIWLQAADPL TDAQKEAAHT AAADRARLDL ADADRRRKVE ADRVEAARVK
KAADAVLKPV TLTATRMPTE DDGKLKTPSG ARIPSSAADG NWSVPATKQV NAGLTLKIPL
NKLKSVPKSV MEHNNSVALE SELKAWTDAV RTSLGITTDE AWIDALIPFI GWCCNNGTSD
KHAENQVMQI DSGKGAVTEM SLSPFIVHAR MNGGLRRIMR NYSDETVLLI TNNKLVAHWS
MKHGASANAK YAFDFFVPRS WMNPQDIEVS KQARLAALGT GTYNTMLTSD TTNLRKTTNH
RVLDSDGHPE LT
