RDRP_PMMVJ
ID RDRP_PMMVJ Reviewed; 1612 AA.
AC P89657; P90347;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 94.
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 Pepper mild mottle virus (strain Japan) (PMMV-J).
OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC Martellivirales; Virgaviridae; Tobamovirus.
OX NCBI_TaxID=138663;
OH NCBI_TaxID=3906; Vicia faba (Broad bean) (Faba vulgaris).
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Kirita M., Akutsu K., Watanabe Y., Tsuda S.;
RT "Nucleotide sequence of the Japanese isolate of pepper [Capsicum annuum]
RT mild mottle tobamovirus (TMV-P) RNA.";
RL Nihon Shokubutsu Byori Gakkaiho 63:373-376(1997).
RN [2]
RP INTERACTION WITH HOST PROTEIN TM-1, AND ACTIVITY REGULATION.
RX PubMed=19423673; DOI=10.1073/pnas.0809105106;
RA Ishibashi K., Naito S., Meshi T., Ishikawa M.;
RT "An inhibitory interaction between viral and cellular proteins underlies
RT the resistance of tomato to nonadapted tobamoviruses.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:8778-8783(2009).
RN [3]
RP MUTAGENESIS OF VAL-299; PHE-976 AND ASP-1098.
RX PubMed=24299004; DOI=10.1111/mpp.12107;
RA Mizumoto H., Morikawa Y., Ishibashi K., Kimura K., Matsumoto K.,
RA Tokunaga M., Kiba A., Ishikawa M., Okuno T., Hikichi Y.;
RT "Functional characterization of the mutations in Pepper mild mottle virus
RT overcoming tomato tm-1-mediated resistance.";
RL Mol. Plant Pathol. 15:479-487(2014).
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 -!- ACTIVITY REGULATION: In resistant plants, is bound by host protein Tm-1
CC (e.g. tomato Tm-1 AC A7M6E7), thereby inhibiting replication complex
CC activity. {ECO:0000269|PubMed:19423673}.
CC -!- SUBUNIT: Heterodimer of a large and a small subunit (By similarity).
CC Both large and small subunits interact, via an ATP bridge, with host
CC protein Tm-1 (e.g. tomato Tm-1 AC A7M6E7 and AC A7M6E8)
CC (PubMed:19423673). {ECO:0000250, ECO:0000269|PubMed:19423673}.
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-1117 and Gln-
CC 1119, 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}.
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DR EMBL; AB000709; BAA19167.1; -; mRNA.
DR EMBL; AB000709; BAA19166.1; -; mRNA.
DR RefSeq; NP_619741.1; NC_003630.1.
DR SMR; P89657; -.
DR PRIDE; P89657; -.
DR GeneID; 1724829; -.
DR KEGG; vg:1724829; -.
DR Proteomes; UP000000475; 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; Host-virus interaction; Hydrolase;
KW Nucleotide-binding; Nucleotidyltransferase; RNA suppression of termination;
KW RNA-directed RNA polymerase; Suppressor of RNA silencing; Transferase;
KW Viral RNA replication.
FT CHAIN 1..1612
FT /note="Replicase large subunit"
FT /id="PRO_0000041180"
FT CHAIN 1..1117
FT /note="Replicase small subunit"
FT /id="PRO_0000041181"
FT DOMAIN 72..280
FT /note="Alphavirus-like MT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
FT DOMAIN 803..964
FT /note="(+)RNA virus helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00990"
FT DOMAIN 965..1117
FT /note="(+)RNA virus helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00990"
FT DOMAIN 1380..1493
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 52..466
FT /note="Methyltransferase"
FT REGION 831..1086
FT /note="Helicase"
FT BINDING 838..843
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P03587,
FT ECO:0000255|PROSITE-ProRule:PRU00990"
FT BINDING 870
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P03587"
FT BINDING 968..969
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P03587"
FT BINDING 1077
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P03587"
FT BINDING 1098..1101
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P03587"
FT MUTAGEN 299
FT /note="V->R: Increased ability to multiply in tomato plants
FT but reduced infectivity in original host plants (e.g.
FT pepper and tobacco); when associated with Y-976 and N-
FT 1098."
FT /evidence="ECO:0000269|PubMed:24299004"
FT MUTAGEN 976
FT /note="F->Y: Increased ability to multiply in tomato plants
FT but reduced infectivity in original host plants (e.g.
FT pepper and tobacco); when associated with R-299 and N-
FT 1098."
FT /evidence="ECO:0000269|PubMed:24299004"
FT MUTAGEN 1098
FT /note="D->N: Weaker inhibitory effect of the tomato tm-1
FT protein and enhanced viral replication efficiency in tomato
FT plants. On the contrary, abolished replication in tobacco
FT plants. Increased ability to multiply in tomato plants but
FT reduced infectivity in original host plants (e.g. pepper
FT and tobacco); when associated with R-299 and Y-976."
FT /evidence="ECO:0000269|PubMed:24299004"
SQ SEQUENCE 1612 AA; 183305 MW; E7E66CE8ED81FE4C CRC64;
MAYTQQATNA ALASTLRGNN PLVNDLANRR LYESAVEQCN AHDRRPKVNF LRSISEEQTL
IATKAYPEFQ ITFYNTQNAV HSLAGGLRSL ELEYLMMQIP YGSTTYDIGG NFAAHMFKGR
DYVHCCMPNM DLRDVMRHNA QKDSIELYLS KLAQKKKVIP PYQKPCFDKY TDDPQSVVCS
KPFQHCEGVS HCTDKVYAVA LHSLYDIPAD EFGAALLRRN VHVCYAAFHF SENLLLEDSY
VSLDDIGAFF SREGDMLNFS FVAESTLNYT HSYSNVLKYV CKTYFPASSR EVYMKEFLVT
RVNTWFCKFS RLDTFVLYRG VYHRGVDKEQ FYSAMEDAWH YKKTLAMMNS ERILLEDSSS
VNYWFPKMKD MVIVPLFDVS LQNEGKRLAR KEVMVSKDFV YTVLNHIRTY QSKALTYANV
LSFVESIRSR VIINGVTARS EWDVDKALLQ SLSMTFFLQT KLAMLKDDLV VQKFQVHSKS
LTEYVWDEIT AAFHNCFPTI KERLINKKLI TVSEKALEIK VPDLYVTFHD RLVKEYKSSV
EMPVLDVKKS LEEAEVMYNA LSEISILKDS DKFDVDVFSR MCNTLGVDPL VAAKVMVAVV
SNESGLTLTF ERPTEANVAL ALQPTITSKE EGSLKIVSSD VGESSIKEVV RKSEISMLGL
TGNTVSDEFQ RSTEIESLQQ FHMVSTETII RKQMHAMVYT GPLKVQQCKN YLDSLVASLS
AAVSNLKKII KDTAAIDLET KEKFGVYDVC LKKWLVKPLS KGHAWGVVMD SDYKCFVALL
TYDGENIVCG ETWRRVAVSS ESLVYSDMGK IRAIRSVLKD GEPHISSAKV TLVDGVPGCG
KTKEILSRVN FDEDLVLVPG KQAAEMIRRR ANSSGLIVAT KENVRTVDSF LMNYGRGPCQ
YKRLFLDEGL MLHPGCVNFL VGMSLCSEAF VYGDTQQIPY INRVATFPYP KHLSQLEVDA
VETRRTTLRC PADITFFLNQ KYEGQVMCTS SVTRSVSHEV IQGAAVMNPV SKPLKGKVIT
FTQSDKSLLL SRGYEDVHTV HEVQGETFED VSLVRLTPTP VGIISKQSPH LLVSLSRHTR
SIKYYTVVLD AVVSVLRDLE CVSSYLLDMY KVDVSTQYQL QIESVYKGVN LFVAAPKTGD
VSDMQYYYDK CLPGNSTILN EYDAVTMQIR ENSLNVKDCV LDMSKSVPLP RESETTLKPV
IRTAAEKPRK PGLLENLVAM IKRNFNSPEL VGVVDIEDTA SLVVDKFFDA YLIKEKKKPK
NIPLLSRASL ERWIEKQEKS TIGQLADFDF IDLPAVDQYR HMIKQQPKQR LDLSIQTEYP
ALQTIVYHSK KINALFGPVF SELTRQLLET IDSSRFMFYT RKTPTQIEEF FSDLDSNVPM
DILELDISKY DKSQNEFHCA VEYEIWKRLG LDDFLAEVWK HGHRKTTLKD YTAGIKTCLW
YQRKSGDVTT FIGNTIIIAA CLSSMLPMER LIKGAFCGDD SILYFPKGTD FPDIQQGANL
LWNFEAKLFR KRYGYFCGRY IIHHDRGCIV YYDPLKLISK LGAKHIKNRE HLEEFRTSLC
DVAGSLNNCA YYTHLDDAVG EVIKTAPPGS FVYRALVKYL CDKRLFQTLF LE
