ID   RDRP_TMVRA              Reviewed;        1616 AA.
AC   Q98745; O41340;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1997, sequence version 1.
DT   03-AUG-2022, entry version 93.
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 Rakkyo) (TMV-R).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Martellivirales; Virgaviridae; Tobamovirus.
OX   NCBI_TaxID=138310;
OH   NCBI_TaxID=130426; Allium chinense.
OH   NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=8678834; DOI=10.1007/bf01718163;
RA   Chen J., Watanabe Y., Sako N., Ohsima K., Okada Y.;
RT   "Complete nucleotide sequence and synthesis of infectious in vitro
RT   transcripts from a full-length cDNA clone of a rakkyo strain of tobacco
RT   mosaic virus.";
RL   Arch. Virol. 141:885-900(1996).
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; D63809; BAA09876.1; -; Genomic_RNA.
DR   EMBL; D63809; BAA09877.1; -; Genomic_RNA.
DR   Proteomes; UP000008251; 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; Reference proteome; 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_0000041170"
FT   CHAIN           1..1116
FT                   /note="Replicase small subunit"
FT                   /id="PRO_0000041171"
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;  183582 MW;  AC7CF5429EBAD49A CRC64;
     MAYTQTATTS ALLDTVRGNN SLVNDLAKRR LYDTAVDEFN ARDRRPKVNF SKVISEEQTL
     IATRAYPEFQ ITFYNTQNAV HSLAGGLRSL ELEYLMMQIP YGSLTYDIGG NFASHLFKGR
     AYVHCCMPNL DVRDIMRHEG QKDSIELYLS RLDRGGKTVP NFQKEAFDRY AEFPEDAVCH
     NTFQTCEHQP MQQSGKVYAI ALHSIYDIPA DEFGAALLRK NVHTCYAAFH FSENLLLEDS
     YVNLDEINAC FSRDGDKLTF SFASESTLNY CHSFSNILKY VCKTYFPASN REVYMKEFLV
     TRVNTWFCKF SRIDTFLLYK GVAHKSVDSE QFYTAMEDAW HYKKTLAMCN SERILLEDSS
     SVNYWFPKMR DMVIIPLFDI SLETSKRSRK EVLVSKDFVF TVLNHIRTYQ AKALTYANVL
     SFVESIRSRV IINGVTARSE WDVDKSLLQS LSMTFFLHTK LAVLKDDLLI SKFSLGSKTV
     CQHVWDEISL AFGNAFPSVK ERLLNKKLIR AAGDALEIKV PDLYITFHDR LVAEYKSSVD
     MPALDIRKRM EETEVMYNAL SELSVLRESD KFDVDVFSQM CKSLEVDPMT AAKVIVAVMS
     NESGLTLTFE RPTEANVAQA LQDQEKASEG ALVVTSREVE EPSMKGSMAR GELQLAGFAG
     DHPESSYSRN EEIESLEQFH MATADSLIRK QMSSIVYTGP IKVQQMKNFI DSLVASLSAA
     VSNLVKILKD TAAIDLETRQ KFGVLDVASR KWLIKPTAKS HAWGVVETHA RKYHVALLEY
     DEQGIVTCDD WRRVAVSSES VVYSDMAKLR TLRRLLRDGE PHVSNAKVVL VDGVPGCGKT
     KEILSRVNFD EDLILVPGKQ AAEMIRRRAN SSGIIVATKD NVRTVDSFMM NFGKTTRCQF
     KRLFIDEGLM LHTGCVNFLV AMSLCDVAYV YGDTQQIPYI NRVSGFPYPA HFSKLEVDEV
     ETRRTTLRCP ADVTHYLNRR YEGFVVSTSS VKKSVSQEMV SGAAVINPIS KPLHGKILTF
     TQSDKEALLS RGYSEVHTVH EVQGETYSDV SLVRLTPTPI SIIAGDSPHV LVALSRHTCS
     LKYYTVVMDP LVSIIRDLEK LSSYLLDMYK VDAGIQXQLQ IDSVFKGSNL FVAAPKTGDI
     SDMQFYYDKC LPGNSTMMNN FDAVTMRLTD ISLNVKDCIL DMSKSVAAPK DQIKPLIPMV
     RTAAEMPRQT GLLENLVAMI KRNFNAPELS GIIDIENTAS LVVDKFFDSY LLKEKRKPNK
     NVSLFSRESL NRWLEKQERV TIGQLADFDF VDLPAVDQYR HMIKAQPKQK LDTSIQTEYP
     ALQTIVYHSK KINAIFGPLF SELTRQLLDS VDSSRFLFFT RKTPAQIEDF FGDLDSHVPM
     DVLELDISKY DKSQNEFHCA VEYEIWRRLG FEDFLGEVWK QGHRKTTLKD YTAGIKTCIW
     YQRKSGDVTT FIGNTVIIAA CLASMLRMEK IIKGAFCGDD SLLYFPKGCE FPDIQHSVNL
     MWNFEAKLFK KQYGYFCGRY IIHHDRGCIV YYDPLKLISK LGAKHIKDWE HLEEFRRSLC
     DVAVSLNNCA YYTQLDDAVW EVHKTAPPGS FVYKSLVKYL SDKVLFRSLF INGSSC