ID   RDRP_TRVPP              Reviewed;        1707 AA.
AC   Q9J942; Q9QPN5;
DT   31-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2001, sequence version 2.
DT   23-FEB-2022, entry version 91.
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=194 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=134 kDa protein;
DE     AltName: Full=Methyltransferase/RNA helicase;
OS   Tobacco rattle virus (isolate PpK20) (TRV).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Martellivirales; Virgaviridae; Tobravirus.
OX   NCBI_TaxID=652939;
OH   NCBI_TaxID=42337; Bidens pilosa (Hairy beggarticks) (Cobbler's pegs).
OH   NCBI_TaxID=4072; Capsicum annuum (Capsicum pepper).
OH   NCBI_TaxID=59895; Cynara cardunculus var. scolymus (Globe artichoke) (Cynara scolymus).
OH   NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RA   Visser P.B., Bol J.F.;
RT   "Complete nucleotide sequence of RNA 1 of tobacco rattle virus isolate
RT   PpK20.";
RL   Submitted (JUL-1999) 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).
CC       {ECO:0000305}.
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   -!- 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   -!- SUBUNIT: Heterodimer of a large and a small subunit. {ECO:0000250}.
CC   -!- MISCELLANEOUS: The replicase large subunit is translated as a fusion
CC       protein by episodic readthrough of a termination codon. When
CC       readthrough of the terminator codon TGA occurs between the codons for
CC       1187-Lys and 1189-Arg, this results in the addition of the RdRp region.
CC   -!- SIMILARITY: Belongs to the ssRNA positive-strand viruses RNA-directed
CC       RNA polymerase family. {ECO:0000305}.
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DR   EMBL; AF166084; AAD48026.1; -; Genomic_RNA.
DR   EMBL; AF166084; AAD48027.2; -; Genomic_RNA.
DR   RefSeq; NP_620669.1; NC_003805.1.
DR   GeneID; 962130; -.
DR   KEGG; vg:962130; -.
DR   Proteomes; UP000001669; 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:UniProtKB-KW.
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; Coiled coil; Helicase; Hydrolase; Methyltransferase;
KW   Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW   RNA-binding; RNA-directed RNA polymerase; Transferase;
KW   Viral RNA replication.
FT   CHAIN           1..1707
FT                   /note="Replicase large subunit"
FT                   /id="PRO_0000409292"
FT   CHAIN           1..1187
FT                   /note="Replicase small subunit"
FT                   /id="PRO_0000409293"
FT   DOMAIN          86..300
FT                   /note="Alphavirus-like MT"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
FT   DOMAIN          872..1033
FT                   /note="(+)RNA virus helicase ATP-binding"
FT   DOMAIN          1034..1187
FT                   /note="(+)RNA virus helicase C-terminal"
FT   DOMAIN          1449..1562
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          65..425
FT                   /note="Methyltransferase"
FT   REGION          901..1155
FT                   /note="Helicase"
FT   COILED          601..622
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   1707 AA;  194180 MW;  15900BC7CE9BC8AE CRC64;
     MANGNFKLSQ LLNVDEMSAE QRSHFFDLML TKPDCEIGQM MQRVVVDKVD DMIRERKTKD
     PVIVHEVLSQ KEQNKLMEIY PEFNIVFKDD KNMVHGFAAA ERKLQALLLL DRVPALQEVD
     DIGGQWSFWV TRGEKRIHSC CPNLDIRDDQ REISRQIFLT AIGDQARSGK RQMSENELWM
     YDQFRKNIAA PNAVRCNNTY HGCTCRGFSD GKKKGAQYAI ALHSLYDFKL KDLMATMVEK
     KTKVGHAAML FAPESMLVDE GPLPSVDGYY MKKNGKIYFG FEKDPSFSYI HDWEEYKKYL
     LGKPVSYQGN VFYFEPWQVR GDTMLFSIYR IAGVPRRSLS SQEYYRRIYI SRWENMVVVP
     IFDLVESTRE LVKKDLFVEK QFMDKCLDYI ARLSDQQLTI SNVKSYLSSN NWVLFINGAA
     VKNKQSVDSR DLQLLAQTLL VKEQVARPVM RELREAILTE TKPITSLTDV LGLISRKMWK
     QFANKIAVGG FVGMVGTLIG FYPKKVLTWA KDTPNGPELC YENSHKTKVI VFLSVVYAIG
     GITLMRRDIR DGLVKKLCDM FDIKRGAHVL DVENPCRYYD INDFFSSLYS ASESGETVLP
     DLSEVKAKSD KLLQQKKEIA DEFLSAKFSN YSGSSVRTSP PSVVGSSRSG LGLLLEDSNV
     LTQARVGVSR KVADEEIMEQ FLSGLIDTEA EIDEVVPAFS AECERGETSG TKVLCNLLTP
     PGFENVLPAV KPLVSKGKTV KRVDYFQVMG GERLPKRPVV SGDDSVDARR EFLYYLDAER
     VAQNDEIMSL YRDYSRGVIR TGGQNYPHGL GVWDVEMKNW CIRPVVTEHA YVSNPDKRMD
     DWSGYLEVAV WERGMLVNDF AVERMSDYVI VCDQTYLCNN RLILDNLSAL DLGPVNCSFE
     LVDGVPGCGK STMIVNSANP CVDVVLSTGR AATDDLIERF ASKGFPCKLK RRVKTVDSFL
     MHCVDGSLTG DVLHFDEALM AHAGMVYFCA QIAGAKRCIC QGDQNQISFK PRVSQVDLRF
     SSLVGKFDIV TEKRETYRSP ADVAAVLNKY YTGDVRTHNA TANSMTVRKI VSKEQVSLKP
     GAQYITFLQS EKKELVNLLA LRKVAAKVST VHESQGETFK DVVLVRTKPT DDSIARGREY
     LIVALSRHTQ SLVYETVKED DVSKEIRESA ALTKAALARF FVTETVLXRF RSRFDVFRHH
     EGPCAVPDSG TITDLEMWYD ALFPGNSLRD SSLDGYLVAT TDCNLRLDNV TIKSGNWKDK
     FAEKETFLKP VIRTAMPDKR KTTQLESLLA LQKRNQAAPD LQENVHATVL IEETMKKLKS
     VVYDVGKIRA DPIVNRAQME RWWRNQSTAV QAKVVADVRE LHEIDYSSYM FMIKSDVKPK
     TDLTPQFEYS ALQTVVYHEK LINSLFGPIF KEINERKLDA MQPHFVFNTR MTSSDLNDRV
     KFLNTEAAYD FVEIDMSKFD KSANRFHLQL QLEIYRLFGL DEWAAFLWEV SHTQTTVRDI
     QNGMMAHIWY QQKSGDADTY NANSDRTLCA LLSELPLEKA VMVTYGGDDS LIAFPRGTQF
     VDPCPKLATK WNFECKIFKY DVPMFCGKFL LKTSSCYEFV PDPVKVLTKL GKKSIKDVQH
     LAEIYISLND SNRALGNYMV VSKLSESVSD RYLYKGDSVH ALCALWKHIK SFTALCTLFR
     DENDKELNPA KVDWKKAQRA VSNFYDW