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Protein

Replicase large subunit

Gene
N/A
Organism
Tomato mosaic virus (strain L) (ToMV) (TMV strain tomato)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Replicase large subunit: is an RNA-dependent RNA polymerase active in viral RNA replication.1 Publication
Replicase small subunit: is a methyltransferase active in RNA capping and an RNA helicase. Methyltransferase displays a cytoplasmic capping enzyme activity. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. Helicase region probably exhibits NTPase and RNA unwinding activities (Potential). It also acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. May mediate silencing suppression through either inhibition of HEN1-mediated siRNA or siRNA demethylation (By similarity).By similarityCurated

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi833 – 8408ATPSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nucleotidyltransferase, RNA-directed RNA polymerase, Suppressor of RNA silencing, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Replicase large subunit (EC:2.1.1.-, EC:2.7.7.-, EC:2.7.7.48, EC:3.6.4.13)
Alternative name(s):
183 kDa protein
RNA-directed RNA polymerase
Cleaved into the following chain:
Alternative name(s):
126 kDa protein
Methyltransferase/RNA helicase
Short name:
MT/HEL
OrganismiTomato mosaic virus (strain L) (ToMV) (TMV strain tomato)
Taxonomic identifieri12252 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageVirgaviridaeTobamovirus
Virus hostiAntirrhinum majus (Garden snapdragon) [TaxID: 4151]
Capsicum (peppers) [TaxID: 4071]
Delphinium [TaxID: 46246]
Petunia [TaxID: 4101]
Solanum lycopersicum (Tomato) (Lycopersicon esculentum) [TaxID: 4081]
Tagetes (marigolds) [TaxID: 13707]
Proteomesi
  • UP000001451 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi349 – 3491C → A: Loss of RNA silencing suppression activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 16161616Replicase large subunitPRO_0000041194Add
BLAST
Chaini1 – 11161116Replicase small subunitPRO_0000041195Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit (By similarity). May interact with the host proteins TOM1 and ARL8.By similarity

Structurei

Secondary structure

1
1616
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi672 – 6754Combined sources
Helixi676 – 6794Combined sources
Helixi684 – 6874Combined sources
Helixi701 – 72929Combined sources
Beta strandi730 – 7323Combined sources
Beta strandi740 – 7467Combined sources
Turni747 – 7504Combined sources
Beta strandi751 – 7544Combined sources
Beta strandi756 – 7583Combined sources
Beta strandi762 – 7687Combined sources
Beta strandi773 – 7775Combined sources
Beta strandi782 – 7843Combined sources
Beta strandi791 – 7977Combined sources
Helixi798 – 8003Combined sources
Helixi804 – 81310Combined sources
Beta strandi817 – 8193Combined sources
Beta strandi826 – 8338Combined sources
Helixi839 – 8468Combined sources
Turni849 – 8513Combined sources
Beta strandi853 – 8575Combined sources
Helixi859 – 86911Combined sources
Turni870 – 8723Combined sources
Turni879 – 8813Combined sources
Beta strandi882 – 8843Combined sources
Helixi885 – 8906Combined sources
Turni891 – 8933Combined sources
Beta strandi894 – 8963Combined sources
Beta strandi901 – 9055Combined sources
Helixi908 – 9103Combined sources
Helixi913 – 92210Combined sources
Beta strandi926 – 9327Combined sources
Helixi950 – 9534Combined sources
Beta strandi958 – 9636Combined sources
Beta strandi965 – 9684Combined sources
Helixi971 – 9788Combined sources
Beta strandi981 – 9833Combined sources
Beta strandi995 – 9995Combined sources
Helixi1003 – 10053Combined sources
Turni1008 – 10103Combined sources
Beta strandi1015 – 10217Combined sources
Helixi1022 – 10298Combined sources
Turni1030 – 10323Combined sources
Beta strandi1034 – 10385Combined sources
Helixi1040 – 10423Combined sources
Beta strandi1047 – 10548Combined sources
Helixi1068 – 10747Combined sources
Beta strandi1075 – 108713Combined sources
Helixi1090 – 110011Combined sources
Helixi1103 – 11075Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3VKWX-ray1.90A666-1111[»]
3WRXX-ray2.50C/D666-1116[»]
3WRYX-ray2.30C/D666-1116[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini72 – 281210Alphavirus-like MTPROSITE-ProRule annotationAdd
BLAST
Domaini801 – 963163(+)RNA virus helicase ATP-bindingAdd
BLAST
Domaini964 – 1116153(+)RNA virus helicase C-terminalAdd
BLAST
Domaini1380 – 1493114RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni50 – 458409MethyltransferaseAdd
BLAST
Regioni830 – 1085256HelicaseAdd
BLAST

Sequence similaritiesi

Contains 1 alphavirus-like MT (methyltransferase) domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR002588. Alphavirus-like_MT_dom.
IPR027417. P-loop_NTPase.
IPR007094. RNA-dir_pol_PSvirus.
IPR001788. Tymovirus_RNA-dep_RNA_pol.
[Graphical view]
PfamiPF00978. RdRP_2. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF01660. Vmethyltransf. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51743. ALPHAVIRUS_MT. 1 hit.
PS51657. PSRV_HELICASE. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P03587-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAYTQTATSS ALLETVRGNN TLVNDLAKRR LYDTAVDEFN ARDRRPKVNF
60 70 80 90 100
SKVVSEEQTL IATKAYPEFQ ITFYNTQNAV HSLAGGLRSL ELEYLMMQIP
110 120 130 140 150
YGSLTYDIGG NFASHLFKGR AYVHCCMPNL DVRDIMRHEG QKDSIELYLS
160 170 180 190 200
RLERGNKHVP NFQKEAFDRY AEMPNEVVCH DTFQTCRHSQ ECYTGRVYAI
210 220 230 240 250
ALHSIYDIPA DEFGAALLRK NVHVCYAAFH FSENLLLEDS HVNLDEINAC
260 270 280 290 300
FQRDGDRLTF SFASESTLNY SHSYSNILKY VCKTYFPASN REVYMKEFLV
310 320 330 340 350
TRVNTWFCKF SRIDTFLLYK GVAHKGVDSE QFYKAMEDAW HYKKTLAMCN
360 370 380 390 400
SERILLEDSS SVNYWFPKMR DMVIVPLFDI SLETSKRTRK EVLVSKDFVY
410 420 430 440 450
TVLNHIRTYQ AKALTYSNVL SFVESIRSRV IINGVTARSE WDVDKSLLQS
460 470 480 490 500
LSMTFFLHTK LAVLKDDLLI SKFALGPKTV SQHVWDEISL AFGNAFPSIK
510 520 530 540 550
ERLINRKLIK ITENALEIRV PDLYVTFHDR LVSEYKMSVD MPVLDIRKKM
560 570 580 590 600
EETEEMYNAL SELSVLKNSD KFDVDVFSQM CQSLEVDPMT AAKVIVAVMS
610 620 630 640 650
NESGLTLTFE QPTEANVALA LQDSEKASDG ALVVTSRDVE EPSIKGSMAR
660 670 680 690 700
GELQLAGLSG DVPESSYTRS EEIESLEQFH MATASSLIHK QMCSIVYTGP
710 720 730 740 750
LKVQQMKNFI DSLVASLSAA VSNLVKILKD TAAIDLETRQ KFGVLDVASK
760 770 780 790 800
RWLVKPSAKN HAWGVVETHA RKYHVALLEH DEFGIITCDN WRRVAVSSES
810 820 830 840 850
VVYSDMAKLR TLRRLLKDGE PHVSSAKVVL VDGVPGCGKT KEILSRVNFE
860 870 880 890 900
EDLILVPGRQ AAEMIRRRAN ASGIIVATKD NVRTVDSFLM NYGKGARCQF
910 920 930 940 950
KRLFIDEGLM LHTGCVNFLV EMSLCDIAYV YGDTQQIPYI NRVTGFPYPA
960 970 980 990 1000
HFAKLEVDEV ETRRTTLRCP ADVTHFLNQR YEGHVMCTSS EKKSVSQEMV
1010 1020 1030 1040 1050
SGAASINPVS KPLKGKILTF TQSDKEALLS RGYADVHTVH EVQGETYADV
1060 1070 1080 1090 1100
SLVRLTPTPV SIIARDSPHV LVSLSRHTKS LKYYTVVMDP LVSIIRDLER
1110 1120 1130 1140 1150
VSSYLLDMYK VDAGTQXQLQ VDSVFKNFNL FVAAPKTGDI SDMQFYYDKC
1160 1170 1180 1190 1200
LPGNSTLLNN YDAVTMKLTD ISLNVKDCIL DMSKSVAAPK DVKPTLIPMV
1210 1220 1230 1240 1250
RTAAEMPRQT GLLENLVAMI KRNFNSPELS GVVDIENTAS LVVDKFFDSY
1260 1270 1280 1290 1300
LLKEKRKPNK NFSLFSRESL NRWIAKQEQV TIGQLADFDF VDLPAVDQYR
1310 1320 1330 1340 1350
HMIKAQPKQK LDLSIQTEYP ALQTIVYHSK KINAIFGPLF SELTRQLLDS
1360 1370 1380 1390 1400
IDSSRFLFFT RKTPAQIEDF FGDLDSHVPM DVLELDVSKY DKSQNEFHCA
1410 1420 1430 1440 1450
VEYEIWRRLG LEDFLAEVWK QGHRKTTLKD YTAGIKTCLW YQRKSGDVTT
1460 1470 1480 1490 1500
FIGNTVIIAS CLASMLPMEK LIKGAFCGDD SLLYFPKGCE YPDIQQAANL
1510 1520 1530 1540 1550
MWNFEAKLFK KQYGYFCGRY VIHHDRGCIV YYDPLKLISK LGAKHIKDWD
1560 1570 1580 1590 1600
HLEEFRRSLC DVAESLNNCA YYTQLDDAVG EVHKTAPPGS FVYKSLVKYL
1610
SDKVLFRSLF LDGSSC
Length:1,616
Mass (Da):183,567
Last modified:December 1, 2000 - v2
Checksum:iA8EC8929B5CF7CAF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02144 Genomic RNA. Translation: CAA26085.1.
X02144 Genomic RNA. Translation: CAA26082.1.
PIRiA04195. WMTM8T.
RefSeqiNP_078446.1. NC_002692.1.
NP_078447.1. NC_002692.1.

Genome annotation databases

GeneIDi920838.
920841.
KEGGivg:920838.
vg:920841.

Keywords - Coding sequence diversityi

RNA suppression of termination

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02144 Genomic RNA. Translation: CAA26085.1.
X02144 Genomic RNA. Translation: CAA26082.1.
PIRiA04195. WMTM8T.
RefSeqiNP_078446.1. NC_002692.1.
NP_078447.1. NC_002692.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3VKWX-ray1.90A666-1111[»]
3WRXX-ray2.50C/D666-1116[»]
3WRYX-ray2.30C/D666-1116[»]
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi920838.
920841.
KEGGivg:920838.
vg:920841.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR002588. Alphavirus-like_MT_dom.
IPR027417. P-loop_NTPase.
IPR007094. RNA-dir_pol_PSvirus.
IPR001788. Tymovirus_RNA-dep_RNA_pol.
[Graphical view]
PfamiPF00978. RdRP_2. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF01660. Vmethyltransf. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51743. ALPHAVIRUS_MT. 1 hit.
PS51657. PSRV_HELICASE. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Nucleotide sequence of the tobacco mosaic virus (tomato strain) genome and comparison with the common strain genome."
    Ohno T., Aoyagi M., Yamanashi Y., Saito H., Ikawa S., Meshi T., Okada Y.
    J. Biochem. 96:1915-1923(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Tomato mosaic virus replication protein suppresses virus-targeted posttranscriptional gene silencing."
    Kubota K., Tsuda S., Tamai A., Meshi T.
    J. Virol. 77:11016-11026(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF CYS-349.
  3. "Crystal structure of the superfamily 1 helicase from Tomato mosaic virus."
    Nishikiori M., Sugiyama S., Xiang H., Niiyama M., Ishibashi K., Inoue T., Ishikawa M., Matsumura H., Katoh E.
    J. Virol. 86:7565-7576(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 666-1111, INTERACTION WITH HOST PROTEINS TOM1 AND ARL8.

Entry informationi

Entry nameiRDRP_TOML
AccessioniPrimary (citable) accession number: P03587
Secondary accession number(s): O41352
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: December 1, 2000
Last modified: June 24, 2015
This is version 86 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This protein is translated as a fusion protein by episodic readthrough of a termination codon. When readthrough of the terminator codon TGA occurs between the codons for Gln-1116 and Gln-1118, this results in the addition of the RdRp region to the replicase.

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.