ID   RDRP_TOMK1              Reviewed;        1616 AA.
AC   Q9Q1T8; Q9Q1T7;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-2000, sequence version 2.
DT   03-AUG-2022, entry version 88.
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   Tomato mosaic virus (strain Kazakh K1) (ToMV) (TMV strain K1).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Martellivirales; Virgaviridae; Tobamovirus.
OX   NCBI_TaxID=138311;
OH   NCBI_TaxID=4151; Antirrhinum majus (Garden snapdragon).
OH   NCBI_TaxID=4071; Capsicum (peppers).
OH   NCBI_TaxID=46246; Delphinium.
OH   NCBI_TaxID=4101; Petunia.
OH   NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
OH   NCBI_TaxID=13707; Tagetes (marigolds).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=10732356;
RA   Belenovich E.V., Novikov V.K., Zavriev S.K.;
RT   "Biological properties and genome structure of the Kazakh isolate K1 of
RT   Tobacco Mosaic virus.";
RL   Mol. Biol. (Mosk.) 34:172-176(2000).
CC   -!- FUNCTION: [Replicase large subunit]: Is an RNA-dependent RNA polymerase
CC       active in viral RNA replication.
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       terminator codon TGA occurs between the codons for Gln-1116 and Gln-
CC       1118, this results in the addition of the RdRp region to the replicase.
CC   -!- SIMILARITY: Belongs to the ssRNA positive-strand viruses RNA-directed
CC       RNA polymerase family. {ECO:0000305}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AJ243571; CAB62911.1; -; Genomic_RNA.
DR   EMBL; AJ243571; CAB62912.1; -; Genomic_RNA.
DR   Proteomes; UP000008252; 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_0000041190"
FT   CHAIN           1..1116
FT                   /note="Replicase small subunit"
FT                   /id="PRO_0000041191"
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   REGION          830..1085
FT                   /note="Helicase"
FT   BINDING         833..840
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   1616 AA;  183609 MW;  4BF9913CE791DE33 CRC64;
     MAYTQTATSS ALLETVRGNN TLVNDLAKRR LYDTAVDEFN ARDRRPKVNF SKVVSEEQTL
     IATKAYPEFQ ITFYNTQNAV HSLAGGLRSL ELEYLMMQIP YGSLTYDIGG NFASHLFKGR
     AYVHCCMPNL DVRDIMRHEG QKDSIELYLS RLERGNKHVP NFQKEAFDRY AEMPNEVVCH
     DTFQTCRHSQ ECYTGRVYAI ALHSIYDIPA DEFGAALLRK NVHVCYAAFH FSENLLLEDS
     HVNLDEINAC FQRDGDRLTF SFASESTLNY SHSYSNILKY VCKTYFPASN REVYMKEFLV
     TRVNTWFCKF SRIDTFLLYK GVAHKGVDNE QFYKAMEDAW HYKKTLAMCN SERILLEDSS
     SVNYWFPKMR DMVIVPLFDI SLETSKRTRK EVLVSKDFVY TVLNHIRTYQ AKALTYSNVL
     SFVESIRSRV IINGVTARSE WDVDKSLLQS LSMTFFLHTK LAVLKDDLLI SKFALGPKTV
     SQHVWDEISL AFGNAFPSIK ERLINRKLIK ITENALEIRV PDLYVTFHDR LVSEYKMSVD
     MPVLDIRKKM EETEEMYNAL SELSVLKTSD KFDVDVFSQM CQSLEVDPMT AAKVIVAVMS
     NESGLTLTFE QPTEANVALA LQDSEKASDG ALVVTSRDVE EPSIRGSMAR GELQLAGLSG
     DVPESSYTRS EEIESLEQFH MATASSLIHK QMCSIVYTGP LKVQQMKNFI DSLVASLSAA
     VSNLVKILKD TAAIDLETRQ KFGVLDVASK RWLVKPSAKN HAWGVVETHA RKYHVALLEH
     DEFGIITCDN WRRVAVSSES VVYSDMAKLR TLRRLLKDGE PHVSSAKVVL VDGVPGCGKT
     KEILSRVNFE EDLILVPGRQ AAEMIRRRAN ASGIIVATKD NVRTVDSFLM NYGKGARCQF
     KRLFIDEGLM LHTGCVNFLV EMSLCDIAYV YGDTQQIPYI NRVTGFPYPA HFAKLEVDEV
     ETRRTTLRCP ADVTHFLNQR YEGHVMCTSS EKKSVSQEMV SGAASINPVS KPLKGKILTF
     TQSDKEALLS RGYADVHTVH EVQGETYADV SLVRLTPTPV SIIARDSPHV LVSLSRHTKS
     LKYYTVVMDP LVSIIRDLER VSSYLLDMYK VDAGTQXQLQ VDSVFKNFNL FVAAPKTGDI
     SDMQFYYDKC LPGNSTLLNN YDAVTMKLTD ISLNVKDCIL DMSKSVAAPK DVKPTLIPMV
     RTAAEMPRQT GLLENLVAMI KRNFNSPELS GVVDIENTAS LVVDKFFDSY LLKEKRKPNK
     NFSLFSRESL NRWIAKQEQV TIGQLADFDF VDLPAVDQYR HMIKAQPKQK LDLSIQTEYP
     ALQTIVYHSK KINAIFGPLF SELTRQLLDS IDSSRFLFFT RKTPAQIEDF FGDLDSHVPM
     DVLELDVSKY DKSQNEFHCA VEYEIWRRLG LEDFLAEVWK QGHRKTTLKD YTAGIKTCLW
     YQRKSGDVTT FIGNTVIIAS CLASMLPMEK LIKGAFCGDD SLLYFPKGCE YPDIQQAANL
     MWNFEAKLFK KQYGYFCGRY VIHHDRGCIV YYDPLKLISK LGAKHIKDWD HLEEFRRSLC
     DVAESLNNCA YYTQLDDAVG EVHKTAPPGS FVYKSLVKYL SDKVLFRSLF LDGSSC