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Q12009

- TRMB_YEAST

UniProt

Q12009 - TRMB_YEAST

Protein

tRNA (guanine-N(7)-)-methyltransferase

Gene

TRM8

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 112 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Methyltransferase that catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA, a modification required to maintain stability of tRNAs; its absence resulting in tRNA decay. Both the D-stem and T-stem structures of tRNAs are required for efficient methyltransferase activity.2 PublicationsUniRule annotation

    Catalytic activityi

    S-adenosyl-L-methionine + guanine(46) in tRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(46) in tRNA.1 PublicationUniRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei103 – 1031S-adenosyl-L-methionine; via carbonyl oxygen1 PublicationUniRule annotation
    Binding sitei181 – 1811S-adenosyl-L-methionine; via carbonyl oxygen1 PublicationUniRule annotation
    Active sitei184 – 1841Curated

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. tRNA (guanine-N7-)-methyltransferase activity Source: UniProtKB-HAMAP
    3. tRNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. RNA (guanine-N7)-methylation Source: GOC
    2. tRNA methylation Source: SGD

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    RNA-binding, S-adenosyl-L-methionine, tRNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:YDL201W-MONOMER.
    UniPathwayiUPA00989.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA (guanine-N(7)-)-methyltransferaseUniRule annotation (EC:2.1.1.33UniRule annotation)
    Alternative name(s):
    Transfer RNA methyltransferase 8UniRule annotation
    tRNA (guanine(46)-N(7))-methyltransferaseUniRule annotation
    tRNA(m7G46)-methyltransferaseUniRule annotation
    Gene namesi
    Name:TRM8UniRule annotation
    Ordered Locus Names:YDL201W
    ORF Names:D1075
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDL201w.
    SGDiS000002360. TRM8.

    Subcellular locationi

    Nucleus 1 PublicationUniRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell
    2. tRNA methyltransferase complex Source: SGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 286286tRNA (guanine-N(7)-)-methyltransferasePRO_0000171437Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei7 – 71Phosphoserine; by ATM or ATR1 Publication
    Modified residuei59 – 591Phosphoserine2 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ12009.
    PaxDbiQ12009.
    PeptideAtlasiQ12009.

    Expressioni

    Gene expression databases

    GenevestigatoriQ12009.

    Interactioni

    Subunit structurei

    Forms a complex with TRM82.1 PublicationUniRule annotation

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    TRM82Q037742EBI-19552,EBI-19486

    Protein-protein interaction databases

    BioGridi31845. 48 interactions.
    DIPiDIP-8614N.
    IntActiQ12009. 1 interaction.
    MINTiMINT-2782058.
    STRINGi4932.YDL201W.

    Structurei

    Secondary structure

    1
    286
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi63 – 653
    Helixi73 – 753
    Helixi78 – 803
    Helixi83 – 853
    Turni88 – 914
    Beta strandi92 – 943
    Beta strandi97 – 1026
    Helixi108 – 1169
    Beta strandi120 – 1278
    Helixi129 – 14416
    Beta strandi147 – 1504
    Turni151 – 1544
    Beta strandi155 – 1595
    Helixi166 – 1683
    Beta strandi175 – 1828
    Helixi199 – 20810
    Beta strandi209 – 22012
    Helixi222 – 23413
    Beta strandi238 – 2403
    Helixi243 – 2475
    Helixi250 – 2578
    Helixi260 – 2678
    Beta strandi273 – 2797

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2VDUX-ray2.40E/F39-286[»]
    2VDVX-ray2.30E/F47-286[»]
    ProteinModelPortaliQ12009.
    SMRiQ12009. Positions 60-286.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ12009.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni126 – 1272S-adenosyl-L-methionine binding
    Regioni161 – 1622S-adenosyl-L-methionine binding
    Regioni259 – 2613S-adenosyl-L-methionine binding

    Sequence similaritiesi

    Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0220.
    GeneTreeiENSGT00390000017840.
    HOGENOMiHOG000260965.
    KOiK03439.
    OMAiRAHSNPI.
    OrthoDBiEOG708W9T.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    HAMAPiMF_03055. tRNA_methyltr_TrmB_euk.
    InterProiIPR029063. SAM-dependent_MTases-like.
    IPR025763. Trm8_euk.
    IPR003358. tRNA_(Gua-N-7)_MeTrfase.
    [Graphical view]
    PfamiPF02390. Methyltransf_4. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00091. TIGR00091. 1 hit.
    PROSITEiPS51625. SAM_MT_TRMB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q12009-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKAKPLSQDP GSKRYAYRIN KEENRKELKH VKINESSLVQ EGQKIDLPKK    50
    RYYRQRAHSN PFSDHQLEYP VSPQDMDWSK LYPYYKNAEN GQMTKKVTIA 100
    DIGCGFGGLM IDLSPAFPED LILGMEIRVQ VTNYVEDRII ALRNNTASKH 150
    GFQNINVLRG NAMKFLPNFF EKGQLSKMFF CFPDPHFKQR KHKARIITNT 200
    LLSEYAYVLK EGGVVYTITD VKDLHEWMVK HLEEHPLFER LSKEWEENDE 250
    CVKIMRNATE EGKKVERKKG DKFVACFTRL PTPAIL 286
    Length:286
    Mass (Da):33,391
    Last modified:November 1, 1996 - v1
    Checksum:i0280B9A7B02C85B7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X99000 Genomic DNA. Translation: CAA67468.1.
    Z74249 Genomic DNA. Translation: CAA98779.1.
    BK006938 Genomic DNA. Translation: DAA11663.1.
    PIRiS67760.
    RefSeqiNP_010080.1. NM_001180261.1.

    Genome annotation databases

    EnsemblFungiiYDL201W; YDL201W; YDL201W.
    GeneIDi851326.
    KEGGisce:YDL201W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X99000 Genomic DNA. Translation: CAA67468.1 .
    Z74249 Genomic DNA. Translation: CAA98779.1 .
    BK006938 Genomic DNA. Translation: DAA11663.1 .
    PIRi S67760.
    RefSeqi NP_010080.1. NM_001180261.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2VDU X-ray 2.40 E/F 39-286 [» ]
    2VDV X-ray 2.30 E/F 47-286 [» ]
    ProteinModelPortali Q12009.
    SMRi Q12009. Positions 60-286.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31845. 48 interactions.
    DIPi DIP-8614N.
    IntActi Q12009. 1 interaction.
    MINTi MINT-2782058.
    STRINGi 4932.YDL201W.

    Proteomic databases

    MaxQBi Q12009.
    PaxDbi Q12009.
    PeptideAtlasi Q12009.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDL201W ; YDL201W ; YDL201W .
    GeneIDi 851326.
    KEGGi sce:YDL201W.

    Organism-specific databases

    CYGDi YDL201w.
    SGDi S000002360. TRM8.

    Phylogenomic databases

    eggNOGi COG0220.
    GeneTreei ENSGT00390000017840.
    HOGENOMi HOG000260965.
    KOi K03439.
    OMAi RAHSNPI.
    OrthoDBi EOG708W9T.

    Enzyme and pathway databases

    UniPathwayi UPA00989 .
    BioCyci YEAST:YDL201W-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q12009.
    NextBioi 968378.
    PROi Q12009.

    Gene expression databases

    Genevestigatori Q12009.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    HAMAPi MF_03055. tRNA_methyltr_TrmB_euk.
    InterProi IPR029063. SAM-dependent_MTases-like.
    IPR025763. Trm8_euk.
    IPR003358. tRNA_(Gua-N-7)_MeTrfase.
    [Graphical view ]
    Pfami PF02390. Methyltransf_4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53335. SSF53335. 1 hit.
    TIGRFAMsi TIGR00091. TIGR00091. 1 hit.
    PROSITEi PS51625. SAM_MT_TRMB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA."
      Alexandrov A., Martzen M.R., Phizicky E.M.
      RNA 8:1253-1266(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, INTERACTION WITH TRM82.
    4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. "tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p."
      Alexandrov A., Grayhack E.J., Phizicky E.M.
      RNA 11:821-830(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, TRNA-BINDING, INTERACTION WITH TRM82.
    7. "Rapid tRNA decay can result from lack of nonessential modifications."
      Alexandrov A., Chernyakov I., Gu W., Hiley S.L., Hughes T.R., Grayhack E.J., Phizicky E.M.
      Mol. Cell 21:87-96(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "RNA recognition mechanism of eukaryote tRNA (m7G46) methyltransferase (Trm8-Trm82 complex)."
      Matsumoto K., Toyooka T., Tomikawa C., Ochi A., Takano Y., Takayanagi N., Endo Y., Hori H.
      FEBS Lett. 581:1599-1604(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    10. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 29-286 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE AND TRM82, SUBUNIT, PROBABLE ACTIVE SITE.

    Entry informationi

    Entry nameiTRMB_YEAST
    AccessioniPrimary (citable) accession number: Q12009
    Secondary accession number(s): D6VRF3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2003
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 112 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 2630 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3