ID   RDRP_TMV                Reviewed;        1616 AA.
AC   P03586; O41341;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-2000, sequence version 2.
DT   03-AUG-2022, entry version 113.
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 vulgare) (TMV) (Tobacco mosaic virus (strain
OS   U1)).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Martellivirales; Virgaviridae; Tobamovirus.
OX   NCBI_TaxID=12243;
OH   NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=6964389; DOI=10.1073/pnas.79.19.5818;
RA   Goelet P., Lomonossoff G.P., Butler P.J.G., Akam M.E., Gait M.J., Karn J.;
RT   "Nucleotide sequence of tobacco mosaic virus RNA.";
RL   Proc. Natl. Acad. Sci. U.S.A. 79:5818-5822(1982).
RN   [2]
RP   CHARACTERIZATION.
RX   PubMed=10814574; DOI=10.1006/viro.2000.0313;
RA   Lewandowski D.J., Dawson W.O.;
RT   "Functions of the 126- and 183-kDa proteins of tobacco mosaic virus.";
RL   Virology 271:90-98(2000).
RN   [3]
RP   INTERACTION WITH NICOTIANA TABACUM ADC1A.
RC   STRAIN=cv. Xanthi;
RX   DOI=10.1007/s10327-004-0139-2;
RA   Shimizu T., Yamaji Y., Ogasawara Y., Hamada K., Sakurai K., Kobayashi T.,
RA   Watanabe T., Hibi T.;
RT   "Interaction between the helicase domain of the tobacco mosaic virus
RT   replicase and a tobacco arginine decarboxylase.";
RL   J. Gen. Plant Pathol. 70:353-358(2004).
RN   [4]
RP   FUNCTION OF THE REPLICASE SMALL SUBUNIT, AND MUTAGENESIS OF CYS-349.
RX   PubMed=17634237; DOI=10.1128/jvi.00727-07;
RA   Vogler H., Akbergenov R., Shivaprasad P.V., Dang V., Fasler M., Kwon M.-O.,
RA   Zhanybekova S., Hohn T., Heinlein M.;
RT   "Modification of small RNAs associated with suppression of RNA silencing by
RT   tobamovirus replicase protein.";
RL   J. Virol. 81:10379-10388(2007).
CC   -!- FUNCTION: [Replicase large subunit]: Is an RNA-dependent RNA polymerase
CC       active in viral RNA replication. {ECO:0000269|PubMed:17634237}.
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. {ECO:0000269|PubMed:17634237, 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. Interacts, via its
CC       helicase region, with the Nicotiana tabacum arginine decarboxylase 1A
CC       (ADC1A) C-terminal internal region (Ref.3). {ECO:0000269|Ref.3}.
CC   -!- INTERACTION:
CC       P03586; Q75WV4: N; Xeno; NbExp=2; IntAct=EBI-3504078, EBI-15623116;
CC       PRO_0000041163; B2C7Y6: NRIP1; Xeno; NbExp=4; IntAct=EBI-1804464, EBI-1809509;
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. {ECO:0000269|PubMed:10814574}.
CC   -!- SIMILARITY: Belongs to the ssRNA positive-strand viruses RNA-directed
CC       RNA polymerase family. {ECO:0000305}.
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DR   EMBL; V01408; CAA24688.1; -; Unassigned_RNA.
DR   EMBL; V01409; -; NOT_ANNOTATED_CDS; Genomic_RNA.
DR   PIR; A04194; WMTM18.
DR   RefSeq; NP_056764.1; NC_001367.1.
DR   BioGRID; 3509210; 1.
DR   DIP; DIP-29269N; -.
DR   IntAct; P03586; 2.
DR   GeneID; 1494081; -.
DR   KEGG; vg:1494081; -.
DR   Proteomes; UP000000522; 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   1: Evidence at protein level;
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_0000041162"
FT   CHAIN           1..1116
FT                   /note="Replicase small subunit"
FT                   /id="PRO_0000041163"
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"
FT   VARIANT         9
FT                   /note="T -> S"
FT   VARIANT         14
FT                   /note="D -> E"
FT   VARIANT         21
FT                   /note="S -> T"
FT   VARIANT         37
FT                   /note="E -> D"
FT   VARIANT         638
FT                   /note="E -> A"
FT   MUTAGEN         349
FT                   /note="C->A: Loss of RNA silencing suppression activity."
FT                   /evidence="ECO:0000269|PubMed:17634237"
SQ   SEQUENCE   1616 AA;  183468 MW;  6DE2F2B11F5550CE CRC64;
     MAYTQTATTS ALLDTVRGNN SLVNDLAKRR LYDTAVEEFN ARDRRPKVNF SKVISEEQTL
     IATRAYPEFQ ITFYNTQNAV HSLAGGLRSL ELEYLMMQIP YGSLTYDIGG NFASHLFKGR
     AYVHCCMPNL DVRDIMRHEG QKDSIELYLS RLERGGKTVP NFQKEAFDRY AEIPEDAVCH
     NTFQTMRHQP 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 CQSLEVDPMT AAKVIVAVMS
     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 KPLHGKILTF
     TQSDKEALLS RGYSDVHTVH EVQGETYSDV SLVRLTPTPV SIIAGDSPHV LVALSRHTCS
     LKYYTVVMDP LVSIIRDLEK LSSYLLDMYK VDAGTQXQLQ IDSVFKGSNL FVAAPKTGDI
     SDMQFYYDKC LPGNSTMMNN FDAVTMRLTD ISLNVKDCIL DMSKSVAAPK DQIKPLIPMV
     RTAAEMPRQT GLLENLVAMI KRNFNAPELS GIIDIENTAS LVVDKFFDSY LLKEKRKPNK
     NVSLFSRESL NRWLEKQEQV TIGQLADFDF VDLPAVDQYR HMYKAQPKQK LDTSIQTEYP
     ALQTIVYHSK KINAIFGPLF 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