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Protein

tRNA (guanine(9)-N1)-methyltransferase

Gene

TRM10

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent guanine N(1)-methyltransferase that catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs.3 Publications

Catalytic activityi

S-adenosyl-L-methionine + guanine9 in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine9 in tRNA.2 Publications

Kineticsi

kcat is 0.54 min(-1) for tRNA(Gly GCC) and 0.31 min(-1) for tRNA(Val UAC) (m1G9)-methylation, respectively.1 Publication

  1. KM=2400 nM for tRNA(Gly GCC)1 Publication
  2. KM=1860 nM for tRNA(Val UAC)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei206 – 2061S-adenosyl-L-methionine; via amide nitrogen
    Active sitei210 – 2101Proton acceptor1 Publication
    Binding sitei218 – 2181S-adenosyl-L-methionine
    Binding sitei232 – 2321S-adenosyl-L-methionine; via amide nitrogen

    GO - Molecular functioni

    GO - Biological processi

    • tRNA methylation Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16684.
    YEAST:G3O-33493-MONOMER.
    BRENDAi2.1.1.221. 984.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA (guanine(9)-N1)-methyltransferase1 Publication (EC:2.1.1.2212 Publications)
    Alternative name(s):
    tRNA methyltransferase 101 Publication
    tRNA(m1G9)-methyltransferase1 Publication
    Short name:
    tRNA(m1G9)MTase1 Publication
    Gene namesi
    Name:TRM101 Publication
    Ordered Locus Names:YOL093WImported
    ORF Names:O0926
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XV

    Organism-specific databases

    EuPathDBiFungiDB:YOL093W.
    SGDiS000005453. TRM10.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi118 – 1181Q → A: Completely abolishes catalytic activity. 1 Publication
    Mutagenesisi209 – 2091V → A: Reduces catalytic activity. 1 Publication
    Mutagenesisi210 – 2101D → N: Completely abolishes catalytic activity. 1 Publication
    Mutagenesisi211 – 2111K → A: Reduces catalytic activity. 1 Publication
    Mutagenesisi212 – 2121N → A: Has weaker affinity for S-adenosyl-L-methionine and reduces catalytic activity by 90%. 1 Publication
    Mutagenesisi247 – 2471T → A: Reduces catalytic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 293293tRNA (guanine(9)-N1)-methyltransferasePRO_0000060520Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei16 – 161PhosphothreonineCombined sources
    Modified residuei283 – 2831PhosphoserineCombined sources

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ12400.

    PTM databases

    iPTMnetiQ12400.

    Interactioni

    Subunit structurei

    Monomer.By similarity

    Protein-protein interaction databases

    BioGridi34309. 45 interactions.
    DIPiDIP-4737N.
    IntActiQ12400. 1 interaction.
    MINTiMINT-548089.

    Structurei

    Secondary structure

    1
    293
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi91 – 10010Combined sources
    Helixi104 – 1063Combined sources
    Helixi109 – 12820Combined sources
    Beta strandi129 – 13911Combined sources
    Helixi142 – 1509Combined sources
    Helixi153 – 1553Combined sources
    Helixi157 – 1593Combined sources
    Beta strandi163 – 1653Combined sources
    Beta strandi167 – 1693Combined sources
    Helixi170 – 1734Combined sources
    Beta strandi176 – 1783Combined sources
    Helixi180 – 1823Combined sources
    Beta strandi183 – 1864Combined sources
    Beta strandi191 – 1933Combined sources
    Beta strandi202 – 2065Combined sources
    Helixi217 – 2259Combined sources
    Beta strandi229 – 2313Combined sources
    Helixi235 – 2373Combined sources
    Helixi248 – 25811Combined sources
    Turni259 – 2624Combined sources
    Helixi264 – 2718Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4JWJX-ray1.76A/B84-276[»]
    ProteinModelPortaliQ12400.
    SMRiQ12400. Positions 84-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini83 – 279197SAM-dependent MTase TRM10-typePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni186 – 1872S-adenosyl-L-methionine binding
    Regioni210 – 2145S-adenosyl-L-methionine binding
    Regioni244 – 2463S-adenosyl-L-methionine binding

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili32 – 6130Sequence analysisAdd
    BLAST

    Sequence similaritiesi

    Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family.PROSITE-ProRule annotation
    Contains 1 SAM-dependent MTase TRM10-type domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    GeneTreeiENSGT00530000063169.
    HOGENOMiHOG000195825.
    InParanoidiQ12400.
    KOiK15445.
    OMAiTSDSPNM.
    OrthoDBiEOG7G4QRH.

    Family and domain databases

    InterProiIPR028564. MT_TRM10-typ.
    IPR007356. tRNA_m1G_MeTrfase_euk.
    IPR016653. tRNA_MeTfrase_TRM10.
    IPR016009. tRNA_MeTrfase_TRMD/TRM10.
    [Graphical view]
    PANTHERiPTHR13563. PTHR13563. 1 hit.
    PfamiPF01746. tRNA_m1G_MT. 1 hit.
    [Graphical view]
    PIRSFiPIRSF016323. tRNA_m1G_mtfrase_met. 1 hit.
    PROSITEiPS51675. SAM_MT_TRM10. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q12400-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSNDEINQNE EKVKRTPPLP PVPEGMSKKQ WKKMCKRQRW EENKAKYNAE
    60 70 80 90 100
    RRVKKKRLRH ERSAKIQEYI DRGEEVPQEL IREPRINVNQ TDSGIEIILD
    110 120 130 140 150
    CSFDELMNDK EIVSLSNQVT RAYSANRRAN HFAEIKVAPF DKRLKQRFET
    160 170 180 190 200
    TLKNTNYENW NHFKFLPDDK IMFGDEHISK DKIVYLTADT EEKLEKLEPG
    210 220 230 240 250
    MRYIVGGIVD KNRYKELCLK KAQKMGIPTR RLPIDEYINL EGRRVLTTTH
    260 270 280 290
    VVQLMLKYFD DHNWKNAFES VLPPRKLDAE AKSASSSPAP KDT
    Length:293
    Mass (Da):34,520
    Last modified:November 1, 1996 - v1
    Checksum:iC3DC7C4BB2FFBE63
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X83121 Genomic DNA. Translation: CAA58186.1.
    Z74835 Genomic DNA. Translation: CAA99105.1.
    BK006948 Genomic DNA. Translation: DAA10691.1.
    PIRiS57376.
    RefSeqiNP_014548.1. NM_001183347.1.

    Genome annotation databases

    EnsemblFungiiYOL093W; YOL093W; YOL093W.
    GeneIDi854060.
    KEGGisce:YOL093W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X83121 Genomic DNA. Translation: CAA58186.1.
    Z74835 Genomic DNA. Translation: CAA99105.1.
    BK006948 Genomic DNA. Translation: DAA10691.1.
    PIRiS57376.
    RefSeqiNP_014548.1. NM_001183347.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4JWJX-ray1.76A/B84-276[»]
    ProteinModelPortaliQ12400.
    SMRiQ12400. Positions 84-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi34309. 45 interactions.
    DIPiDIP-4737N.
    IntActiQ12400. 1 interaction.
    MINTiMINT-548089.

    PTM databases

    iPTMnetiQ12400.

    Proteomic databases

    MaxQBiQ12400.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYOL093W; YOL093W; YOL093W.
    GeneIDi854060.
    KEGGisce:YOL093W.

    Organism-specific databases

    EuPathDBiFungiDB:YOL093W.
    SGDiS000005453. TRM10.

    Phylogenomic databases

    GeneTreeiENSGT00530000063169.
    HOGENOMiHOG000195825.
    InParanoidiQ12400.
    KOiK15445.
    OMAiTSDSPNM.
    OrthoDBiEOG7G4QRH.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16684.
    YEAST:G3O-33493-MONOMER.
    BRENDAi2.1.1.221. 984.

    Miscellaneous databases

    NextBioi975659.
    PROiQ12400.

    Family and domain databases

    InterProiIPR028564. MT_TRM10-typ.
    IPR007356. tRNA_m1G_MeTrfase_euk.
    IPR016653. tRNA_MeTfrase_TRM10.
    IPR016009. tRNA_MeTrfase_TRMD/TRM10.
    [Graphical view]
    PANTHERiPTHR13563. PTHR13563. 1 hit.
    PfamiPF01746. tRNA_m1G_MT. 1 hit.
    [Graphical view]
    PIRSFiPIRSF016323. tRNA_m1G_mtfrase_met. 1 hit.
    PROSITEiPS51675. SAM_MT_TRM10. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "A 29.425 kb segment on the left arm of yeast chromosome XV contains more than twice as many unknown as known open reading frames."
      Zumstein E., Pearson B.M., Kalogeropoulos A., Schweizer M.
      Yeast 11:975-986(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
      Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
      , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
      Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. "Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9."
      Jackman J.E., Montange R.K., Malik H.S., Phizicky E.M.
      RNA 9:574-585(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    7. Cited for: FUNCTION.
    8. "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 THR-16, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "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-283, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10."
      Swinehart W.E., Henderson J.C., Jackman J.E.
      RNA 19:1137-1146(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    12. "Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate."
      Shao Z., Yan W., Peng J., Zuo X., Zou Y., Li F., Gong D., Ma R., Wu J., Shi Y., Zhang Z., Teng M., Li X., Gong Q.
      Nucleic Acids Res. 42:509-525(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS) OF 84-276 IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF GLN-118; VAL-209; ASP-210; LYS-211; ASN-212 AND THR-247.

    Entry informationi

    Entry nameiTRM10_YEAST
    AccessioniPrimary (citable) accession number: Q12400
    Secondary accession number(s): D6W1X5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 8, 2005
    Last sequence update: November 1, 1996
    Last modified: May 11, 2016
    This is version 118 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 4090 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    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.