ID   RDRP_TMVB               Reviewed;        1616 AA.
AC   Q9YQ08; Q9WKD4;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   03-AUG-2022, entry version 81.
DE   RecName: Full=Replicase large subunit;
DE            EC=2.1.1.-;
DE            EC=2.7.7.-;
DE            EC=2.7.7.48;
DE            EC=3.6.4.13;
DE   AltName: Full=183 kDa protein;
DE   AltName: Full=RNA-directed RNA polymerase;
DE   Contains:
DE     RecName: Full=Replicase small subunit;
DE              EC=2.1.1.-;
DE              EC=2.7.7.-;
DE              EC=3.6.4.13;
DE     AltName: Full=126 kDa protein;
DE     AltName: Full=Methyltransferase/RNA helicase;
DE              Short=MT/HEL;
OS   Tobacco mosaic virus (strain B935A) (TMV).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Martellivirales; Virgaviridae; Tobamovirus.
OX   NCBI_TaxID=138309;
OH   NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RA   Xue C., Zhou X., Chen Q., Qi Y., Li D.;
RT   "Complete nucleotide sequence and genome organization of tobacco mosaic
RT   virus isolated from Vicia faba.";
RL   Submitted (OCT-1998) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: [Replicase large subunit]: Is an RNA-dependent RNA polymerase
CC       active in viral RNA replication. {ECO:0000250}.
CC   -!- FUNCTION: [Replicase small subunit]: Is a methyltransferase active in
CC       RNA capping and an RNA helicase. Methyltransferase displays a
CC       cytoplasmic capping enzyme activity. This function is necessary since
CC       all viral RNAs are synthesized in the cytoplasm, and host capping
CC       enzymes are restricted to the nucleus. Helicase region probably
CC       exhibits NTPase and RNA unwinding activities (Potential). It also acts
CC       as a suppressor of RNA-mediated gene silencing, also known as post-
CC       transcriptional gene silencing (PTGS), a mechanism of plant viral
CC       defense that limits the accumulation of viral RNAs. May mediate
CC       silencing suppression through either inhibition of HEN1-mediated siRNA
CC       or siRNA demethylation (By similarity). {ECO:0000250, ECO:0000305}.
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=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC   -!- SUBUNIT: Heterodimer of a large and a small subunit. {ECO:0000250}.
CC   -!- MISCELLANEOUS: This protein is translated as a fusion protein by
CC       episodic readthrough of a termination codon. When readthrough of the
CC       amber terminator codon TAG occurs between the codons for Gln-1116 and
CC       Gln-1118, this results in the addition of the RdRp region to the
CC       replicase.
CC   -!- SIMILARITY: Belongs to the ssRNA positive-strand viruses RNA-directed
CC       RNA polymerase family. {ECO:0000305}.
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DR   EMBL; AJ011933; CAA09875.1; -; Genomic_RNA.
DR   EMBL; AJ011933; CAA09874.1; -; Genomic_RNA.
DR   Proteomes; UP000000279; Genome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR   GO; GO:0008174; F:mRNA methyltransferase activity; IEA:InterPro.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; 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; -; 2.
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; IPR007094; RNA-dir_pol_PSvirus.
DR   InterPro; IPR001788; Tymovirus_RNA-dep_RNA_pol.
DR   Pfam; PF00978; RdRP_2; 1.
DR   Pfam; PF01443; Viral_helicase1; 1.
DR   Pfam; PF01660; Vmethyltransf; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS51743; ALPHAVIRUS_MT; 1.
DR   PROSITE; PS51657; PSRV_HELICASE; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Helicase; Hydrolase; Nucleotide-binding;
KW   Nucleotidyltransferase; RNA suppression of termination;
KW   RNA-directed RNA polymerase; Suppressor of RNA silencing; Transferase;
KW   Viral RNA replication.
FT   CHAIN           1..1616
FT                   /note="Replicase large subunit"
FT                   /id="PRO_0000041164"
FT   CHAIN           1..1116
FT                   /note="Replicase small subunit"
FT                   /id="PRO_0000041165"
FT   DOMAIN          72..281
FT                   /note="Alphavirus-like MT"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
FT   DOMAIN          801..963
FT                   /note="(+)RNA virus helicase ATP-binding"
FT   DOMAIN          964..1116
FT                   /note="(+)RNA virus helicase C-terminal"
FT   DOMAIN          1380..1493
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          50..458
FT                   /note="Methyltransferase"
FT                   /evidence="ECO:0000255"
FT   REGION          830..1085
FT                   /note="Helicase"
FT                   /evidence="ECO:0000255"
FT   BINDING         833..840
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   1616 AA;  183299 MW;  99A63B441290E6CF CRC64;
     MAYTQTATTS ALLDTVRGNN SLVNDLAKRR LYDTAVEEFN ARDRRPKVNF SKVISEEQTL
     IATRAYPEFQ ITFYNTQNAV HSLAGGLRSL ELEYLMMQIP YGSLTYDIGG NFASHLFKGR
     AYVHCCMPNL DVRDIMRHEG QKDSIELYLS RLERGGKTVP NFQKEAFDRY AEIPEDAVCH
     NTFQTCEHQP MQQSGRVYAI ALHSIYDIPA DEFGAALLRK NVHTCYAAFH FSENLLLEDS
     YVNLDEINAC FSRDGDKLTF SFASESTLNY CHSYSNILKY VCKTYFPASN REVYMKEFLV
     TRVNTWFCKF SRIDTFLLYK GVAHKSVDSE QFYTAMEDAW HYKKTLAMCN SERILLEDSS
     SVNYWFPKMR DMVIVPLFDI SLETSKRTRK EVLVSKDFVF TVLNHIRTYQ AKALTYANVL
     SFVESIRSRV IINGVTARSE WDVDKSLLQS LSMTFYLHTK LAVLKDDLLI SKFSLGSKTV
     CQHVWDEISL AFGNAFPSVK ERLLNRKLIR VAGDALEIRV PDLYVTFHDR LVTEYKASVD
     MPALDIRKKM EETEVMYNAL SELSVLRESD KFDVDVFSQM CKSLEVDPMT AAKVIVADMS
     NESGLTLTFE RPTEANVALA LQDQEKASEG ALVVTSREVE EPSMKGSMAR GELQLAGLAG
     DHPESSYSKN EEIESLEQFH MATADSLIRK QMSSIVYTGP IKVQQMKNFI DSLVASLSAA
     VSNLVKILKD TAAIDLETRQ KFGVLDVASR KWLIKPTAKS HAWGVVETHA RKYHVALLEY
     DEQGVVTCDD WRRVAVSSES VVYSDMAKLR TLRRLLRNGE PHVSSAKVVL VDGVPGCGKT
     KEILSRVNFD EDLILVPGKQ AAEMIRRRAN SSGIIVATKD NVKTVDSFMM NFGKSTRCQF
     KRLFIDEGLM LHTGCVNFLV AMSLCEIAYV YGDTQQIPYI NRVSGFPYPA HFAKLEVDEV
     ETRRTTLRCP ADVTHYLNRR YEGFVMSTSS VKKSVSQEMV GGAAVINPIS KPSHGKILTF
     TQSDKEALLS RGYSDVHTVH EVQGETYSDV SLVRLTPTPV SIIAGDSPHV LVALSRHTCS
     LKYYTVVMDP LVSIIRDLEK LSSYLSDMYK VDAGTQXQLQ IDSVFKGSNL FVAAPKTGDI
     SDMQFYYDKC LPGNSTMMNN FDAVTMRLTD ISLNVKDCIL DMSKSVAAPK DQIKPLIPMV
     RTAAEMPRQT GLLENLVAMI KRNFNAPELS GIIDIENTAS LVVDKFFDSY LLKEKRKPNK
     NVSLFSRESL NRWLEKQEQV TIGQLADFDF VDLPAVDQYR HMIKAQPKQK LDTSIQTEYP
     ALQTIVYHSK KISAIFGPLF SELTRQLLDS VDSSRFLFFT RKTPAQIEDF FGDLDSHVPM
     DVLELDISKY DKSQNEFHCA VEYEIWRRLG FEDFLGEVWK QGHRKTTLKD YTAGIKTCIW
     YQRKSGDVTT FIGNTVIIAA CLASMLPMEK IIKGAFCGDD SLLYFPKGCE FPDVQHSANL
     MWNFEAKLFK KQYGYFCGRY VIHHDRGCIV YYDPLKLISK LGAKHIKDWE HLEEFRRSLC
     DVAVSLNNCA YYTQLDDAVW EVHKTAPPGS FVYKSLVKYL SDKVLFRSLF IDGSSC