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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

Manual assertion based on experiment ini

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

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei206S-adenosyl-L-methionine; via amide nitrogen1
    Active sitei210Proton acceptor1 Publication1
    Binding sitei218S-adenosyl-L-methionine1
    Binding sitei232S-adenosyl-L-methionine; via amide nitrogen1

    GO - Molecular functioni

    GO - Biological processi

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

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciMetaCyc:G3O-33493-MONOMER.
    YEAST:G3O-33493-MONOMER.
    BRENDAi2.1.1.221. 984.
    ReactomeiR-SCE-6782315. tRNA modification in the nucleus and cytosol.

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi118Q → A: Completely abolishes catalytic activity. 1 Publication1
    Mutagenesisi209V → A: Reduces catalytic activity. 1 Publication1
    Mutagenesisi210D → N: Completely abolishes catalytic activity. 1 Publication1
    Mutagenesisi211K → A: Reduces catalytic activity. 1 Publication1
    Mutagenesisi212N → A: Has weaker affinity for S-adenosyl-L-methionine and reduces catalytic activity by 90%. 1 Publication1
    Mutagenesisi247T → A: Reduces catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000605201 – 293tRNA (guanine(9)-N1)-methyltransferaseAdd BLAST293

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei16PhosphothreonineCombined sources1
    Modified residuei283PhosphoserineCombined sources1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ12400.
    PRIDEiQ12400.

    PTM databases

    iPTMnetiQ12400.

    Interactioni

    Subunit structurei

    Monomer.By similarity

    Protein-protein interaction databases

    BioGridi34309. 45 interactors.
    DIPiDIP-4737N.
    IntActiQ12400. 1 interactor.
    MINTiMINT-548089.

    Structurei

    Secondary structure

    1293
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi91 – 100Combined sources10
    Helixi104 – 106Combined sources3
    Helixi109 – 128Combined sources20
    Beta strandi129 – 139Combined sources11
    Helixi142 – 150Combined sources9
    Helixi153 – 155Combined sources3
    Helixi157 – 159Combined sources3
    Beta strandi163 – 165Combined sources3
    Beta strandi167 – 169Combined sources3
    Helixi170 – 173Combined sources4
    Beta strandi176 – 178Combined sources3
    Helixi180 – 182Combined sources3
    Beta strandi183 – 186Combined sources4
    Beta strandi191 – 193Combined sources3
    Beta strandi202 – 206Combined sources5
    Helixi217 – 225Combined sources9
    Beta strandi229 – 231Combined sources3
    Helixi235 – 237Combined sources3
    Helixi248 – 258Combined sources11
    Turni259 – 262Combined sources4
    Helixi264 – 271Combined sources8

    3D structure databases

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

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini83 – 279SAM-dependent MTase TRM10-typePROSITE-ProRule annotationAdd BLAST197

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni186 – 187S-adenosyl-L-methionine binding2
    Regioni210 – 214S-adenosyl-L-methionine binding5
    Regioni244 – 246S-adenosyl-L-methionine binding3

    Coiled coil

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Coiled coili32 – 61Sequence analysisAdd BLAST30

    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.
    OMAiIREPRIN.
    OrthoDBiEOG092C39DJ.

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4JWJX-ray1.76A/B84-276[»]
    ProteinModelPortaliQ12400.
    SMRiQ12400.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi34309. 45 interactors.
    DIPiDIP-4737N.
    IntActiQ12400. 1 interactor.
    MINTiMINT-548089.

    PTM databases

    iPTMnetiQ12400.

    Proteomic databases

    MaxQBiQ12400.
    PRIDEiQ12400.

    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.
    OMAiIREPRIN.
    OrthoDBiEOG092C39DJ.

    Enzyme and pathway databases

    BioCyciMetaCyc:G3O-33493-MONOMER.
    YEAST:G3O-33493-MONOMER.
    BRENDAi2.1.1.221. 984.
    ReactomeiR-SCE-6782315. tRNA modification in the nucleus and cytosol.

    Miscellaneous databases

    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...

    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: November 2, 2016
    This is version 122 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.