ID   POLR_TYMVC              Reviewed;        1844 AA.
AC   P28477;
DT   01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-1992, sequence version 1.
DT   03-AUG-2022, entry version 92.
DE   RecName: Full=RNA replicase polyprotein;
DE   AltName: Full=206 kDa polyprotein;
DE   AltName: Full=206K;
DE   Contains:
DE     RecName: Full=Methyltransferase/Protease/Ubiquitinyl hydrolase;
DE              EC=2.1.1.-;
DE              EC=3.4.19.12 {ECO:0000250|UniProtKB:P10358};
DE              EC=3.4.22.-;
DE     AltName: Full=98 kDa protein;
DE     AltName: Full=MET/PRO;
DE   Contains:
DE     RecName: Full=Putative helicase;
DE              EC=3.6.4.-;
DE     AltName: Full=42 kDa protein;
DE     AltName: Full=HEL;
DE   Contains:
DE     RecName: Full=RNA-directed RNA polymerase;
DE              EC=2.7.7.48;
DE     AltName: Full=66 kDa protein;
DE     AltName: Full=POL;
OS   Turnip yellow mosaic virus (isolate TYMC).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Tymovirales; Tymoviridae; Tymovirus.
OX   NCBI_TaxID=31751;
OH   NCBI_TaxID=3705; Brassica.
OH   NCBI_TaxID=82359; Cardamine lilacina.
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=1731998; DOI=10.1007/bf00034967;
RA   Dreher T.W., Bransom K.L.;
RT   "Genomic RNA sequence of turnip yellow mosaic virus isolate TYMC, a cDNA-
RT   based clone with verified infectivity.";
RL   Plant Mol. Biol. 18:403-406(1992).
CC   -!- FUNCTION: Acts as a cysteine protease, methyltransferase and
CC       deubiquitinase. The cysteine protease activity cleaves the polyprotein
CC       giving rise to mature proteins. The methyltransferase domain is
CC       probably involved in viral RNA capping. The deubiquitylating activity
CC       counteracts the degradation of the viral polymerase mediated by the
CC       host ubiquitin-proteasome system. The polymerase is thus stabilized and
CC       infectivity is increased. Favors K63 poly-Ub linkage.
CC       {ECO:0000250|UniProtKB:P10358}.
CC   -!- FUNCTION: RNA-directed RNA polymerase is responsible for the
CC       replication and transcription of the genome.
CC       {ECO:0000250|UniProtKB:P10358}.
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=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC         and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC         residue protein attached to proteins as an intracellular targeting
CC         signal).; EC=3.4.19.12; Evidence={ECO:0000250|UniProtKB:P10358};
CC   -!- SUBUNIT: Interacts with host ubiquitin. {ECO:0000250|UniProtKB:P10358}.
CC   -!- SUBCELLULAR LOCATION: [Methyltransferase/Protease/Ubiquitinyl
CC       hydrolase]: Host chloroplast envelope {ECO:0000250|UniProtKB:P10358}.
CC   -!- SUBCELLULAR LOCATION: [Putative helicase]: Host chloroplast envelope
CC       {ECO:0000250|UniProtKB:P10358}.
CC   -!- SUBCELLULAR LOCATION: [RNA-directed RNA polymerase]: Host chloroplast
CC       envelope {ECO:0000250|UniProtKB:P10358}.
CC   -!- DOMAIN: [Methyltransferase/Protease/Ubiquitinyl hydrolase]: The viral
CC       OTU domain (vOTU) is responsible for the deubiquitination activity.
CC       Both protease (PRO) and deubiquitination (DUB) activities rely on the
CC       single catalytic site of the cysteine proteinase. The switch in the
CC       PRO/DUB activities is due to the mobility of a GPP flap.
CC       {ECO:0000250|UniProtKB:P10358}.
CC   -!- MISCELLANEOUS: The deubiquitinase activity is low compared to that of
CC       Bunyaviruses or coronaviruses. {ECO:0000250|UniProtKB:P10358}.
CC   -!- SIMILARITY: Belongs to the tymovirus NS35 RNA replicase polyprotein
CC       family. {ECO:0000305}.
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DR   EMBL; X16378; CAA34415.1; -; Genomic_RNA.
DR   PIR; S19151; S19151.
DR   MEROPS; C21.001; -.
DR   PRIDE; P28477; -.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR   GO; GO:0008174; F:mRNA methyltransferase activity; 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:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0006396; P:RNA processing; IEA:InterPro.
DR   GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR   GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR   Gene3D; 3.40.50.300; -; 1.
DR   Gene3D; 3.90.70.100; -; 1.
DR   InterPro; IPR027351; (+)RNA_virus_helicase_core_dom.
DR   InterPro; IPR002588; Alphavirus-like_MT_dom.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR008043; Peptidase_C21.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   InterPro; IPR043629; Salyut_dom.
DR   InterPro; IPR001788; Tymovirus_RNA-dep_RNA_pol.
DR   InterPro; IPR043181; TYMV_endopept_dom.
DR   Pfam; PF05381; Peptidase_C21; 1.
DR   Pfam; PF00978; RdRP_2; 1.
DR   Pfam; PF19227; Salyut; 1.
DR   Pfam; PF01443; Viral_helicase1; 1.
DR   Pfam; PF01660; Vmethyltransf; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS51743; ALPHAVIRUS_MT; 1.
DR   PROSITE; PS51738; PEPTIDASE_C21; 1.
DR   PROSITE; PS51657; PSRV_HELICASE; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Host-virus interaction; Hydrolase; Methyltransferase;
KW   Modulation of host ubiquitin pathway by viral deubiquitinase;
KW   Modulation of host ubiquitin pathway by virus; Multifunctional enzyme;
KW   Nucleotide-binding; Nucleotidyltransferase; Protease;
KW   RNA-directed RNA polymerase; Thiol protease; Transferase;
KW   Viral RNA replication.
FT   CHAIN           1..1844
FT                   /note="RNA replicase polyprotein"
FT                   /id="PRO_0000222940"
FT   CHAIN           1..879
FT                   /note="Methyltransferase/Protease/Ubiquitinyl hydrolase"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
FT                   /id="PRO_0000455972"
FT   CHAIN           880..1259
FT                   /note="Putative helicase"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
FT                   /id="PRO_0000455973"
FT   CHAIN           1260..1844
FT                   /note="RNA-directed RNA polymerase"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
FT                   /id="PRO_0000455974"
FT   DOMAIN          58..219
FT                   /note="Alphavirus-like MT"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
FT   DOMAIN          728..879
FT                   /note="OTU"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
FT   DOMAIN          730..884
FT                   /note="Peptidase C21"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01074"
FT   DOMAIN          946..1103
FT                   /note="(+)RNA virus helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00990"
FT   DOMAIN          1104..1236
FT                   /note="(+)RNA virus helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00990"
FT   DOMAIN          1572..1678
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          571..729
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          859..887
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           865..867
FT                   /note="GPP flap"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
FT   COMPBIAS        571..587
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        598..623
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        624..644
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        673..698
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        783
FT                   /note="For protease activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01074"
FT   ACT_SITE        869
FT                   /note="For protease activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01074"
FT   BINDING         976..983
FT                   /ligand="a ribonucleoside 5'-triphosphate"
FT                   /ligand_id="ChEBI:CHEBI:61557"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00990"
FT   SITE            879..880
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
FT   SITE            1259..1260
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250|UniProtKB:P10358"
SQ   SEQUENCE   1844 AA;  206613 MW;  02CB928FCCCA5EA1 CRC64;
     MAFQLALDAL APTTHRDPSL HPILESTVDS IRSSIQTYPW SIPKELLPLL NSYGIPTSGL
     GTSHHPHAAH KTIETFLLCT HWSFQATTPS SVMFMKPSKF NKLAQVNSNF RELKNYRLHP
     NDSTRYPFTS PDLPVFPTIF MHDALMYYHP SQIMDLFLRK PNLERLYASL VVPPEAHLSD
     QSFYPKLYTY TTTRHTLHYV PEGHEAGSYN QPSDAHSWLR INSIRLGNHH LSVTILESWG
     PVHSLLIQRG TPPPDPSLQA PPTLMASDLF RSYQEPRLDV VSFRIPDAIE LPQATFLQQP
     LRDRLVPRAV YNALFTYTRA VRTLRTSDPA AFVRMHSSKP DHDWVTSNAW DNLQTFALLN
     VPLRPNVVYH VLQSPIASLS LYLRQHWRRL TATAVPILSF LTLLQRFLPL PIPLAEVKSI
     TAFRRELYRK KEPHHPLDVF HLQHRIRNYH SAISAVRPAS PPHQKLPHAL QKAALLLLRP
     ISPLLTATPF FRSEQKSMLP NAELSWTLKR FALPWQASLV LLALSESSIL LHKLFSPPTL
     QAQHDTYHRH LHPGSYSLQW ERTPLSIPRT TAFLPFTPTT STAPPDRSEA SLPPAFASTF
     VPRPPPAASS PGAQPPTTTA APPTPIEPTQ RAHQNSDLAL ESSTSTEPPP PPIRSPDMTP
     SAPVLFPEIN SPRRFPPQLP ATPDLEPAHT PPPLSIPHQD PTDSVDPLMG SHLLHHSLPA
     PPTHPLPSSQ LLPAPLTNDP TAIGPVLPFE ELHPRRYPEN TATFLTRLRS LPSNHLPQPT
     LNCLLSAVSD QTKVSEEHLW ESLQTILPDS QLSNEETNTL GLSTEHLTAL AHLYNFQATV
     YSDRGPILFG PSDTIKRIDI THTTGPPSHF SPGKRLLGSQ PSAKGHPSDP LIRAMKSFKV
     SGNYLPFSEA HNHPTSISHA KNLISNMKNG FDGVLSLLDV STGQRTGPTP KERIIQIDHY
     LDTNPGKTTP VVHFAGFAGC GKTYPIQQLL KTKLFKDFRV SCPTTELRTE WKTAMELHGS
     QSWRFNTWES SILKSSRILV IDEIYKMPRG YLDLSILADP ALELVIILGD PLQGEYHSQS
     KDSSNHRLPS ETLRLLPYID MYCWWSYRIP QCIARLFQIH SFNAWQGVIG SVSTPHDQSP
     VLTNSHASSL TFNSLGYRSC TISSSQGLTF CDPAIIVLDN YTKWLSSANG LVALTRSRSG
     VQFMGPSSYV GGTNGSSAMF SDAFNNSLII MDRYFPSLFP QLKLITSPLT TRGPKLNGAT
     PSASPTHRSP NFHLPPHIPL SYDRDFVTVN STLPDQGPET RLDTHFLPPS RLPLHFDLPP
     AITPPPVSTS VDPPQAKASP VYPGEFFDSL AAFFLPAHDP STREILHKDQ SSNQFPWFDR
     PFSLSCQPSS LISAKHAPNH DPTLLPASIN KRLRFRPSDS PHQITADDVV LGLQLFHSLC
     RAYSRQPNST VPFNPELFAE CISLNEYAQL SSKTQSTIVA NASRSDPDWR HTTVKIFAKA
     QHKVNDGSIF GSWKACQTLA LMHDYVILVL GPVKKYQRIF DNADRPPNIY SHCGKTPNQL
     RDWCQEHLTH STPKIANDYT AFDQSQHGES VVLEALKMKR LNIPSHLIQL HVHLKTNVST
     QFGPLTCMRL TGEPGTYDDN TDYNLAVIYS QYDVGSCPIM VSGDDSLIDH PLPTRHDWPS
     VLKRLHLRFK LELTSHPLFC GYYVGPAGCI RNPLALFCKL MIAVDDDALD DRRLSYLTEF
     TTGHLLGESL WHLLPETHVQ YQSACFDFFC RRCPRHEKML LDDSTPALSL LERITSSPRW
     LTKNAMYLLP AKLRLAITSL SQTQSFPESI EVSHAESELL HYVQ