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P04298

- MCEL_VACCW

UniProt

P04298 - MCEL_VACCW

Protein

mRNA-capping enzyme catalytic subunit

Gene

VACWR106

Organism
Vaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 81 (01 Oct 2014)
      Sequence version 1 (20 Mar 1987)
      Previous versions | rss
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    Functioni

    Catalytic subunit of the mRNA capping enzyme which catalyzes three enzymatic reactions: the 5' triphosphate end of the pre-mRNA is hydrolyzed to a diphosphate by RNA 5' triphosphatase; the diphosphate RNA end is capped with GMP by RNA guanylyltransferase and the GpppN cap is methylated by RNA (guanine-N7) methyltransferase. Heterodimeric mRNA capping enzyme catalyzes the linkage of a N7-methyl-guanosine moiety to the first transcribed nucleotide (cap 0 structure), whereas the polymerase associated VP39 is responsible for a second methylation at the 2'-O position of the ribose (cap 1 structure).
    The heterodimeric enzyme is also involved in early viral gene transcription termination and intermediate viral gene transcription initiation. Early gene transcription termination requires the termination factor VTF, the DNA-dependent ATPase NPH-I and the Rap94 subunit of the viral RNA polymerase, as well as the presence of a specific termination motif. Binds, together with RAP94, to the termination motif 5'-UUUUUNU-3' in the nascent early mRNA.

    Catalytic activityi

    A 5'-phosphopolynucleotide + H2O = a polynucleotide + phosphate.
    GTP + (5')pp-Pur-mRNA = diphosphate + G(5')ppp-Pur-mRNA.
    S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA.PROSITE-ProRule annotation

    Kineticsi

    A-570 and A-763 mutants have 3-fold and 10-fold higher Km values for GpppA.

    1. KM=23 µM for GpppA1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi37 – 371Catalytic; for RNA triphosphatase activitySequence Analysis
    Metal bindingi39 – 391Catalytic; for RNA triphosphatase activitySequence Analysis
    Sitei77 – 771Essential for RNA triphosphatase activity
    Sitei107 – 1071Essential for RNA triphosphatase activity
    Sitei126 – 1261Essential for RNA triphosphatase activity
    Sitei159 – 1591Essential for RNA triphosphatase activity
    Sitei161 – 1611Essential for RNA triphosphatase activity
    Metal bindingi192 – 1921Catalytic; for RNA triphosphatase activitySequence Analysis
    Metal bindingi194 – 1941Catalytic; for RNA triphosphatase activitySequence Analysis
    Active sitei260 – 2601N6-GMP-lysine intermediateSequence Analysis
    Binding sitei573 – 5731S-adenosyl-L-methionine
    Binding sitei598 – 5981S-adenosyl-L-methionine; via carbonyl oxygen
    Sitei607 – 6071mRNA cap bindingPROSITE-ProRule annotation
    Binding sitei620 – 6201S-adenosyl-L-methionine
    Sitei632 – 6321mRNA cap bindingPROSITE-ProRule annotation
    Binding sitei682 – 6821mRNA capPROSITE-ProRule annotation
    Binding sitei763 – 7631mRNA capPROSITE-ProRule annotation
    Binding sitei836 – 8361mRNA capPROSITE-ProRule annotation

    GO - Molecular functioni

    1. GTP binding Source: UniProtKB-KW
    2. metal ion binding Source: UniProtKB-KW
    3. mRNA (guanine-N7-)-methyltransferase activity Source: UniProtKB-EC
    4. mRNA guanylyltransferase activity Source: UniProtKB-EC
    5. polynucleotide 5'-phosphatase activity Source: UniProtKB-EC
    6. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. DNA-templated transcription, termination Source: UniProtKB-KW
    2. regulation of transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase, Methyltransferase, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    mRNA capping, mRNA processing, Transcription, Transcription regulation, Transcription termination

    Keywords - Ligandi

    GTP-binding, Metal-binding, Nucleotide-binding, RNA-binding, S-adenosyl-L-methionine

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    mRNA-capping enzyme catalytic subunit
    Alternative name(s):
    Virus termination factor large subunit
    Short name:
    VTF large subunit
    mRNA-capping enzyme 97 kDa subunit
    mRNA-capping enzyme D1 subunit
    mRNA-capping enzyme large subunit
    Including the following 3 domains:
    Polynucleotide 5'-triphosphatase (EC:3.1.3.33)
    Alternative name(s):
    mRNA 5'-triphosphatase
    Short name:
    TPase
    mRNA guanylyltransferase (EC:2.7.7.50)
    Alternative name(s):
    GTP--RNA guanylyltransferase
    Short name:
    GTase
    mRNA (guanine-N(7)-)-methyltransferase (EC:2.1.1.56)
    Alternative name(s):
    mRNA cap methyltransferase
    Gene namesi
    Ordered Locus Names:VACWR106
    ORF Names:D1R
    OrganismiVaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
    Taxonomic identifieri10254 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePoxviridaeChordopoxvirinaeOrthopoxvirusVaccinia virus
    Virus hostiBos taurus (Bovine) [TaxID: 9913]
    ProteomesiUP000000344: Genome

    Subcellular locationi

    Virion Curated
    Note: All the enzymes and other proteins required to synthesize early mRNAs are packaged within the virion core along with the DNA genome.

    GO - Cellular componenti

    1. virion Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Virion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi77 – 793RTK → ATA: Almost complete loss of RNA triphosphatase activity, 70% loss of guanylyltransferase activity.
    Mutagenesisi107 – 1071K → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication
    Mutagenesisi126 – 1261E → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication
    Mutagenesisi135 – 1362KK → AA: 70% loss of RNA triphosphatase activity, 40% loss of guanylyltransferase activity.
    Mutagenesisi159 – 1591D → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication
    Mutagenesisi161 – 1611K → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication
    Mutagenesisi192 – 1943EIE → AIA: Complete loss of RNA triphosphatase activity, 50% loss of guanylyltransferase activity.
    Mutagenesisi260 – 2601K → A: Complete loss of guanylyltransferase activity, no effect on RNA triphosphatase activity. 1 Publication
    Mutagenesisi524 – 5263KIG → AIA: 50% loss of RNA triphosphatase activity and 40% loss of guanylyltransferase activity.
    Mutagenesisi570 – 5701N → A: Retains substantial methyltransferase activity in vitro; lethal in vivo. 1 Publication
    Mutagenesisi573 – 5731K → A: Complete loss of methyltransferase activity; lethal in vivo. 1 Publication
    Mutagenesisi607 – 6071K → A: Retains substantial methyltransferase activity in vitro; lethal in vivo. 1 Publication
    Mutagenesisi608 – 6081Y → A: Almost complete loss of methyltransferase activity; lethal in vivo. 1 Publication
    Mutagenesisi676 – 6761D → A: Complete loss of methyltransferase activity; lethal in vivo. 1 Publication
    Mutagenesisi679 – 6791F → A: Almost complete loss of methyltransferase activity; lethal in vivo. 1 Publication
    Mutagenesisi682 – 6821H → A: Complete loss of methyltransferase activity; lethal in vivo. 1 Publication
    Mutagenesisi763 – 7631E → A: Retains substantial methyltransferase activity in vitro; lethal in vivo. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 844844mRNA-capping enzyme catalytic subunitPRO_0000210124Add
    BLAST

    Interactioni

    Subunit structurei

    Heterodimer of a catalytic and a regulatory subunit. Intrinsic methyltransferase activity of the catalytic subunit is weak and needs to be stimulated 30- to 50-fold by the regulatory subunit, which is itself catalytically inert.1 Publication

    Protein-protein interaction databases

    DIPiDIP-60664N.

    Structurei

    Secondary structure

    1
    844
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 53
    Helixi11 – 2414
    Beta strandi36 – 449
    Helixi48 – 547
    Beta strandi58 – 6912
    Beta strandi71 – 788
    Helixi82 – 843
    Beta strandi87 – 893
    Helixi92 – 976
    Beta strandi103 – 11614
    Beta strandi119 – 13012
    Helixi134 – 1407
    Beta strandi142 – 15211
    Beta strandi154 – 17017
    Helixi175 – 1817
    Beta strandi182 – 1854
    Beta strandi188 – 1958
    Beta strandi198 – 2003
    Helixi205 – 22016
    Beta strandi226 – 2294
    Beta strandi236 – 2416
    Helixi244 – 2474
    Beta strandi255 – 2595
    Beta strandi262 – 27110
    Beta strandi274 – 2796
    Turni280 – 2823
    Beta strandi283 – 2886
    Beta strandi298 – 31821
    Helixi327 – 33711
    Turni338 – 3403
    Beta strandi343 – 3497
    Helixi359 – 36911
    Turni370 – 3723
    Beta strandi377 – 3848
    Helixi385 – 3884
    Beta strandi389 – 3935
    Beta strandi398 – 4058
    Beta strandi422 – 43211
    Beta strandi435 – 44511
    Beta strandi447 – 4537
    Turni454 – 4574
    Beta strandi458 – 4658
    Helixi466 – 4683
    Beta strandi470 – 48415
    Beta strandi489 – 4924
    Helixi494 – 5029
    Beta strandi508 – 5103
    Helixi511 – 52212
    Helixi525 – 5273
    Helixi563 – 58018
    Turni583 – 5853
    Beta strandi593 – 5964
    Turni600 – 6045
    Helixi605 – 6106
    Beta strandi614 – 6218
    Helixi623 – 63614
    Beta strandi646 – 6516
    Beta strandi656 – 6583
    Helixi659 – 6646
    Beta strandi672 – 6798
    Helixi681 – 6833
    Turni687 – 6893
    Helixi690 – 70011
    Beta strandi701 – 71212
    Helixi714 – 7174
    Beta strandi724 – 7274
    Beta strandi730 – 7323
    Turni734 – 7363
    Beta strandi737 – 7415
    Beta strandi743 – 7453
    Beta strandi748 – 7525
    Turni754 – 7563
    Beta strandi757 – 7593
    Beta strandi761 – 7644
    Helixi768 – 77710
    Beta strandi780 – 7878
    Helixi788 – 7936
    Helixi796 – 8005
    Helixi802 – 8054
    Helixi809 – 82315
    Beta strandi826 – 8283
    Helixi829 – 8335
    Beta strandi836 – 8438

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2VDWX-ray2.70A/C/E/G545-844[»]
    4CKBX-ray2.80A/D1-844[»]
    4CKCX-ray2.90A/D1-844[»]
    4CKEX-ray2.90A/D1-844[»]
    ProteinModelPortaliP04298.
    SMRiP04298. Positions 545-844.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04298.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini516 – 844329mRNA cap 0 methyltransferasePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 539539Triphosphatase-guanylyltransferaseAdd
    BLAST
    Regioni549 – 5502S-adenosyl-L-methionine binding
    Regioni569 – 5702mRNA cap bindingPROSITE-ProRule annotation
    Regioni678 – 6803S-adenosyl-L-methionine binding

    Domaini

    The N-terminus contains the triphosphatase and guanylyltransferase domains, whereas the C-terminus contains the methyltransferase domain. The N-terminus is involved in binding to the temination motif 5'-UUUUUNU-3' in the nascent mRNA.1 Publication

    Sequence similaritiesi

    In the N-terminal section; belongs to the dsDNA virus mRNA guanylyltransferase family.Curated
    In the C-terminal section; belongs to the class I-like SAM-binding methyltransferase superfamily. mRNA cap 0 methyltransferase family.PROSITE-ProRule annotation
    Contains 1 mRNA cap 0 methyltransferase domain.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR019602. mRNA_cap_ATPase/GuylTrfase_vir.
    IPR004971. mRNA_G-N7_MeTrfase_dom.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view]
    PfamiPF10640. Pox_ATPase-GT. 1 hit.
    PF03291. Pox_MCEL. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.
    PROSITEiPS51562. RNA_CAP0_MT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P04298-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDANVVSSST IATYIDALAK NASELEQRST AYEINNELEL VFIKPPLITL    50
    TNVVNISTIQ ESFIRFTVTN KEGVKIRTKI PLSKVHGLDV KNVQLVDAID 100
    NIVWEKKSLV TENRLHKECL LRLSTEERHI FLDYKKYGSS IRLELVNLIQ 150
    AKTKNFTIDF KLKYFLGSGA QSKSSLLHAI NHPKSRPNTS LEIEFTPRDN 200
    ETVPYDELIK ELTTLSRHIF MASPENVILS PPINAPIKTF MLPKQDIVGL 250
    DLENLYAVTK TDGIPITIRV TSNGLYCYFT HLGYIIRYPV KRIIDSEVVV 300
    FGEAVKDKNW TVYLIKLIEP VNAINDRLEE SKYVESKLVD ICDRIVFKSK 350
    KYEGPFTTTS EVVDMLSTYL PKQPEGVILF YSKGPKSNID FKIKKENTID 400
    QTANVVFRYM SSEPIIFGES SIFVEYKKFS NDKGFPKEYG SGKIVLYNGV 450
    NYLNNIYCLE YINTHNEVGI KSVVVPIKFI AEFLVNGEIL KPRIDKTMKY 500
    INSEDYYGNQ HNIIVEHLRD QSIKIGDIFN EDKLSDVGHQ YANNDKFRLN 550
    PEVSYFTNKR TRGPLGILSN YVKTLLISMY CSKTFLDDSN KRKVLAIDFG 600
    NGADLEKYFY GEIALLVATD PDADAIARGN ERYNKLNSGI KTKYYKFDYI 650
    QETIRSDTFV SSVREVFYFG KFNIIDWQFA IHYSFHPRHY ATVMNNLSEL 700
    TASGGKVLIT TMDGDKLSKL TDKKTFIIHK NLPSSENYMS VEKIADDRIV 750
    VYNPSTMSTP MTEYIIKKND IVRVFNEYGF VLVDNVDFAT IIERSKKFIN 800
    GASTMEDRPS TRNFFELNRG AIKCEGLDVE DLLSYYVVYV FSKR 844
    Length:844
    Mass (Da):96,734
    Last modified:March 20, 1987 - v1
    Checksum:i8B9FD3DE836FA6E7
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti705 – 7051G → D in strain: mutant Dts36.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M15058 Genomic DNA. Translation: AAA48253.1.
    AY243312 Genomic DNA. Translation: AAO89385.1.
    PIRiA03872. QQVZ1.
    RefSeqiYP_232988.1. NC_006998.1.

    Genome annotation databases

    GeneIDi3707562.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M15058 Genomic DNA. Translation: AAA48253.1 .
    AY243312 Genomic DNA. Translation: AAO89385.1 .
    PIRi A03872. QQVZ1.
    RefSeqi YP_232988.1. NC_006998.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2VDW X-ray 2.70 A/C/E/G 545-844 [» ]
    4CKB X-ray 2.80 A/D 1-844 [» ]
    4CKC X-ray 2.90 A/D 1-844 [» ]
    4CKE X-ray 2.90 A/D 1-844 [» ]
    ProteinModelPortali P04298.
    SMRi P04298. Positions 545-844.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-60664N.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 3707562.

    Miscellaneous databases

    EvolutionaryTracei P04298.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    InterProi IPR019602. mRNA_cap_ATPase/GuylTrfase_vir.
    IPR004971. mRNA_G-N7_MeTrfase_dom.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view ]
    Pfami PF10640. Pox_ATPase-GT. 1 hit.
    PF03291. Pox_MCEL. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53335. SSF53335. 1 hit.
    PROSITEi PS51562. RNA_CAP0_MT. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence and genetic map of the 16-kb vaccinia virus HindIII D fragment."
      Niles E.G., Condit R.C., Caro P., Davidson K., Matusick L., Seto J.
      Virology 153:96-112(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequencing of the coding region of Vaccinia-WR to an average 9-fold redundancy and an error rate of 0.16/10kb."
      Esposito J.J., Frace A.M., Sammons S.A., Olsen-Rasmussen M., Osborne J., Wohlhueter R.
      Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "Interaction and mutual stabilization of the two subunits of vaccinia virus mRNA capping enzyme coexpressed in Escherichia coli."
      Guo P., Moss B.
      Proc. Natl. Acad. Sci. U.S.A. 87:4023-4027(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SMALL SUBUNIT, PROTEIN SEQUENCE OF 1-20 AND 498-517.
    4. "Intrinsic RNA (guanine-7) methyltransferase activity of the vaccinia virus capping enzyme D1 subunit is stimulated by the D12 subunit. Identification of amino acid residues in the D1 protein required for subunit association and methyl group transfer."
      Mao X., Shuman S.
      J. Biol. Chem. 269:24472-24479(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: DOMAIN METHYLTRANSFERASE.
    5. "Mutational analysis of the RNA triphosphatase component of vaccinia virus mRNA capping enzyme."
      Yu L., Shuman S.
      J. Virol. 70:6162-6168(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE OF TRIPHOSPHATASE ACTIVITY, MUTAGENESIS OF 77-ARG--LYS-79; 135-LYS-LYS-136; 160-PHE-LYS-161; 192-GLU--GLU-194; LYS-260 AND 524-LYS--GLY-526.
    6. "Mapping the active site of vaccinia virus RNA triphosphatase."
      Gong C., Shuman S.
      Virology 309:125-134(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF TRIPHOSPHATASE ACTIVITY, MUTAGENESIS OF LYS-107; GLU-126; ASP-159 AND LYS-161.
    7. "Phenotypic analysis of a temperature sensitive mutant in the large subunit of the vaccinia virus mRNA capping enzyme."
      Shatzer A.N., Kato S.E., Condit R.C.
      Virology 375:236-252(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: IHDW and mutant Dts36.
    8. "Vaccinia virus early gene transcription termination factors VTF and Rap94 interact with the U9 termination motif in the nascent RNA in a transcription ternary complex."
      Christen L.A., Piacente S., Mohamed M.R., Niles E.G.
      Virology 376:225-235(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Structure-function analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase."
      Zheng S., Shuman S.
      RNA 14:696-705(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ASN-570; LYS-573; LYS-607; TYR-608; ASP-676; PHE-679; HIS-682 AND GLU-763.
    10. "Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase."
      De la Pena M., Kyrieleis O.J., Cusack S.
      EMBO J. 26:4913-4925(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 545-844 IN COMPLEX WITH ADOHCY AND THE REGULATORY SUBUNIT.

    Entry informationi

    Entry nameiMCEL_VACCW
    AccessioniPrimary (citable) accession number: P04298
    Secondary accession number(s): Q76ZS6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 1987
    Last sequence update: March 20, 1987
    Last modified: October 1, 2014
    This is version 81 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

    Documents

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

    External Data

    Dasty 3