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Protein

mRNA-capping enzyme catalytic subunit

Gene

VACWR106

Organism
Vaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Cofactori

Mg2+2 Publications

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)DescriptionActionsGraphical viewLength
    Metal bindingi37Magnesium; Catalytic; for RNA triphosphatase activitySequence analysis1 Publication1
    Metal bindingi39Magnesium; Catalytic; for RNA triphosphatase activitySequence analysis1 Publication1
    Sitei77Essential for RNA triphosphatase activity1
    Sitei107Essential for RNA triphosphatase activity1
    Sitei126Essential for RNA triphosphatase activity1
    Sitei159Essential for RNA triphosphatase activity1
    Sitei161Essential for RNA triphosphatase activity1
    Metal bindingi192Magnesium; Catalytic; for RNA triphosphatase activitySequence analysis1 Publication1
    Metal bindingi194Magnesium; Catalytic; for RNA triphosphatase activitySequence analysis1 Publication1
    Active sitei260N6-GMP-lysine intermediateSequence analysis1
    Binding sitei573S-adenosyl-L-methionine1
    Binding sitei598S-adenosyl-L-methionine; via carbonyl oxygen1
    Sitei607mRNA cap bindingPROSITE-ProRule annotation1
    Binding sitei620S-adenosyl-L-methionine1
    Sitei632mRNA cap bindingPROSITE-ProRule annotation1
    Binding sitei682mRNA capPROSITE-ProRule annotation1
    Binding sitei763mRNA capPROSITE-ProRule annotation1
    Binding sitei836mRNA capPROSITE-ProRule annotation1

    GO - Molecular functioni

    • GTP binding Source: UniProtKB-KW
    • metal ion binding Source: UniProtKB-KW
    • mRNA (guanine-N7-)-methyltransferase activity Source: UniProtKB
    • mRNA guanylyltransferase activity Source: UniProtKB-EC
    • polynucleotide 5'-phosphatase activity Source: UniProtKB-EC
    • RNA binding Source: UniProtKB-KW
    • triphosphatase activity Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    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

    Enzyme and pathway databases

    SABIO-RKP04298.

    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]
    Proteomesi
    • UP000000344 Componenti: 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

    • virion Source: UniProtKB-SubCell
    Complete GO annotation...

    Keywords - Cellular componenti

    Virion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi77 – 79RTK → ATA: Almost complete loss of RNA triphosphatase activity, 70% loss of guanylyltransferase activity. 1 Publication3
    Mutagenesisi107K → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication1
    Mutagenesisi126E → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication1
    Mutagenesisi135 – 136KK → AA: 70% loss of RNA triphosphatase activity, 40% loss of guanylyltransferase activity. 1 Publication2
    Mutagenesisi159D → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication1
    Mutagenesisi161K → A: Complete loss of triphosphatase activity, no effect on guanylyltransferase activity. 1 Publication1
    Mutagenesisi192 – 194EIE → AIA: Complete loss of RNA triphosphatase activity, 50% loss of guanylyltransferase activity. 1 Publication3
    Mutagenesisi260K → A: Complete loss of guanylyltransferase activity, no effect on RNA triphosphatase activity. 1 Publication1
    Mutagenesisi524 – 526KIG → AIA: 50% loss of RNA triphosphatase activity and 40% loss of guanylyltransferase activity. 1 Publication3
    Mutagenesisi570N → A: Retains substantial methyltransferase activity in vitro; lethal in vivo. 1 Publication1
    Mutagenesisi573K → A: Complete loss of methyltransferase activity; lethal in vivo. 1 Publication1
    Mutagenesisi607K → A: Retains substantial methyltransferase activity in vitro; lethal in vivo. 1 Publication1
    Mutagenesisi608Y → A: Almost complete loss of methyltransferase activity; lethal in vivo. 1 Publication1
    Mutagenesisi676D → A: Complete loss of methyltransferase activity; lethal in vivo. 1 Publication1
    Mutagenesisi679F → A: Almost complete loss of methyltransferase activity; lethal in vivo. 1 Publication1
    Mutagenesisi682H → A: Complete loss of methyltransferase activity; lethal in vivo. 1 Publication1
    Mutagenesisi763E → A: Retains substantial methyltransferase activity in vitro; lethal in vivo. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002101241 – 844mRNA-capping enzyme catalytic subunitAdd BLAST844

    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

    1844
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi3 – 5Combined sources3
    Helixi11 – 24Combined sources14
    Beta strandi36 – 44Combined sources9
    Helixi48 – 54Combined sources7
    Beta strandi58 – 69Combined sources12
    Beta strandi71 – 78Combined sources8
    Helixi82 – 84Combined sources3
    Beta strandi87 – 89Combined sources3
    Helixi92 – 97Combined sources6
    Beta strandi103 – 116Combined sources14
    Beta strandi119 – 130Combined sources12
    Helixi134 – 140Combined sources7
    Beta strandi142 – 152Combined sources11
    Beta strandi154 – 170Combined sources17
    Helixi175 – 181Combined sources7
    Beta strandi182 – 185Combined sources4
    Beta strandi188 – 195Combined sources8
    Beta strandi198 – 200Combined sources3
    Helixi205 – 220Combined sources16
    Beta strandi226 – 229Combined sources4
    Beta strandi236 – 241Combined sources6
    Helixi244 – 247Combined sources4
    Beta strandi255 – 259Combined sources5
    Beta strandi262 – 271Combined sources10
    Beta strandi274 – 279Combined sources6
    Turni280 – 282Combined sources3
    Beta strandi283 – 288Combined sources6
    Beta strandi298 – 318Combined sources21
    Helixi327 – 337Combined sources11
    Turni338 – 340Combined sources3
    Beta strandi343 – 349Combined sources7
    Helixi359 – 369Combined sources11
    Turni370 – 372Combined sources3
    Beta strandi377 – 384Combined sources8
    Helixi385 – 388Combined sources4
    Beta strandi389 – 393Combined sources5
    Beta strandi398 – 405Combined sources8
    Beta strandi422 – 432Combined sources11
    Beta strandi435 – 445Combined sources11
    Beta strandi447 – 453Combined sources7
    Turni454 – 457Combined sources4
    Beta strandi458 – 465Combined sources8
    Helixi466 – 468Combined sources3
    Beta strandi470 – 484Combined sources15
    Beta strandi489 – 492Combined sources4
    Helixi494 – 502Combined sources9
    Beta strandi508 – 510Combined sources3
    Helixi511 – 522Combined sources12
    Helixi525 – 527Combined sources3
    Helixi563 – 580Combined sources18
    Turni583 – 585Combined sources3
    Beta strandi593 – 596Combined sources4
    Turni600 – 604Combined sources5
    Helixi605 – 610Combined sources6
    Beta strandi614 – 621Combined sources8
    Helixi623 – 636Combined sources14
    Beta strandi646 – 651Combined sources6
    Beta strandi656 – 658Combined sources3
    Helixi659 – 664Combined sources6
    Beta strandi672 – 679Combined sources8
    Helixi681 – 683Combined sources3
    Turni687 – 689Combined sources3
    Helixi690 – 700Combined sources11
    Beta strandi701 – 712Combined sources12
    Helixi714 – 717Combined sources4
    Beta strandi724 – 727Combined sources4
    Beta strandi730 – 732Combined sources3
    Turni734 – 736Combined sources3
    Beta strandi737 – 741Combined sources5
    Beta strandi743 – 745Combined sources3
    Beta strandi748 – 752Combined sources5
    Turni754 – 756Combined sources3
    Beta strandi757 – 759Combined sources3
    Beta strandi761 – 764Combined sources4
    Helixi768 – 777Combined sources10
    Beta strandi780 – 787Combined sources8
    Helixi788 – 793Combined sources6
    Helixi796 – 800Combined sources5
    Helixi802 – 805Combined sources4
    Helixi809 – 823Combined sources15
    Beta strandi826 – 828Combined sources3
    Helixi829 – 833Combined sources5
    Beta strandi836 – 843Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04298.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini516 – 844mRNA cap 0 methyltransferasePROSITE-ProRule annotationAdd BLAST329

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni1 – 539Triphosphatase-guanylyltransferaseAdd BLAST539
    Regioni549 – 550S-adenosyl-L-methionine binding2
    Regioni569 – 570mRNA cap bindingPROSITE-ProRule annotation2
    Regioni678 – 680S-adenosyl-L-methionine binding3

    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.
    [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

            10         20         30         40         50
    MDANVVSSST IATYIDALAK NASELEQRST AYEINNELEL VFIKPPLITL
    60 70 80 90 100
    TNVVNISTIQ ESFIRFTVTN KEGVKIRTKI PLSKVHGLDV KNVQLVDAID
    110 120 130 140 150
    NIVWEKKSLV TENRLHKECL LRLSTEERHI FLDYKKYGSS IRLELVNLIQ
    160 170 180 190 200
    AKTKNFTIDF KLKYFLGSGA QSKSSLLHAI NHPKSRPNTS LEIEFTPRDN
    210 220 230 240 250
    ETVPYDELIK ELTTLSRHIF MASPENVILS PPINAPIKTF MLPKQDIVGL
    260 270 280 290 300
    DLENLYAVTK TDGIPITIRV TSNGLYCYFT HLGYIIRYPV KRIIDSEVVV
    310 320 330 340 350
    FGEAVKDKNW TVYLIKLIEP VNAINDRLEE SKYVESKLVD ICDRIVFKSK
    360 370 380 390 400
    KYEGPFTTTS EVVDMLSTYL PKQPEGVILF YSKGPKSNID FKIKKENTID
    410 420 430 440 450
    QTANVVFRYM SSEPIIFGES SIFVEYKKFS NDKGFPKEYG SGKIVLYNGV
    460 470 480 490 500
    NYLNNIYCLE YINTHNEVGI KSVVVPIKFI AEFLVNGEIL KPRIDKTMKY
    510 520 530 540 550
    INSEDYYGNQ HNIIVEHLRD QSIKIGDIFN EDKLSDVGHQ YANNDKFRLN
    560 570 580 590 600
    PEVSYFTNKR TRGPLGILSN YVKTLLISMY CSKTFLDDSN KRKVLAIDFG
    610 620 630 640 650
    NGADLEKYFY GEIALLVATD PDADAIARGN ERYNKLNSGI KTKYYKFDYI
    660 670 680 690 700
    QETIRSDTFV SSVREVFYFG KFNIIDWQFA IHYSFHPRHY ATVMNNLSEL
    710 720 730 740 750
    TASGGKVLIT TMDGDKLSKL TDKKTFIIHK NLPSSENYMS VEKIADDRIV
    760 770 780 790 800
    VYNPSTMSTP MTEYIIKKND IVRVFNEYGF VLVDNVDFAT IIERSKKFIN
    810 820 830 840
    GASTMEDRPS TRNFFELNRG AIKCEGLDVE DLLSYYVVYV FSKR
    Length:844
    Mass (Da):96,734
    Last modified:March 20, 1987 - v1
    Checksum:i8B9FD3DE836FA6E7
    GO

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural varianti705G → D in strain: mutant Dts36. 1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.
    KEGGivg:3707562.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M15058 Genomic DNA. Translation: AAA48253.1.
    AY243312 Genomic DNA. Translation: AAO89385.1.
    PIRiA03872. QQVZ1.
    RefSeqiYP_232988.1. NC_006998.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-60664N.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneIDi3707562.
    KEGGivg:3707562.

    Enzyme and pathway databases

    SABIO-RKP04298.

    Miscellaneous databases

    EvolutionaryTraceiP04298.

    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.
    [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]
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 93 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

    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.