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Q12093

- MTU1_YEAST

UniProt

Q12093 - MTU1_YEAST

Protein

Mitochondrial tRNA-specific 2-thiouridylase 1

Gene

SLM3

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 116 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Catalyzes the 2-thiolation of uridine at the wobble position (U34) of mitochondrial tRNA(Lys), tRNA(Glu) and tRNA(Gln). Required for the formation of 5-taurinomethyl-2-thiouridine (tm5s2U) of mitochondrial tRNA(Lys), tRNA(Glu), and tRNA(Gln) at the wobble position. ATP is required to activate the C2 atom of the wobble base.3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei58 – 581ATP; via amide nitrogen and carbonyl oxygenBy similarity
    Active sitei127 – 1271NucleophileBy similarity
    Binding sitei154 – 1541ATP; via amide nitrogenBy similarity
    Sitei155 – 1551Interaction with tRNABy similarity
    Active sitei229 – 2291Cysteine persulfide intermediateBy similarity
    Sitei281 – 2811Interaction with tRNABy similarity
    Sitei391 – 3911Interaction with tRNABy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi32 – 398ATPBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. sulfurtransferase activity Source: InterPro
    3. tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity Source: SGD
    4. tRNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. mitochondrial tRNA thio-modification Source: SGD
    2. tRNA methylation Source: GOC

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding, tRNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29458-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Mitochondrial tRNA-specific 2-thiouridylase 1 (EC:2.8.1.-)
    Alternative name(s):
    Mitochondrial translation optimization protein 2
    Synthetic lethal with MSS4 3
    Gene namesi
    Name:SLM3
    Synonyms:MTO2, MTU1
    Ordered Locus Names:YDL033C
    ORF Names:D2761
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDL033c.
    SGDiS000002191. SLM3.

    Subcellular locationi

    Mitochondrion 2 Publications

    GO - Cellular componenti

    1. mitochondrion Source: SGD

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi38 – 381D → A: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 417417Mitochondrial tRNA-specific 2-thiouridylase 1PRO_0000121711Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi127 ↔ 229AlternateBy similarity

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    MaxQBiQ12093.
    PaxDbiQ12093.
    PeptideAtlasiQ12093.

    Expressioni

    Gene expression databases

    GenevestigatoriQ12093.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself1EBI-19558,EBI-19558
    HSP60P198821EBI-19558,EBI-8586

    Protein-protein interaction databases

    BioGridi32024. 150 interactions.
    IntActiQ12093. 2 interactions.
    MINTiMINT-640057.
    STRINGi4932.YDL033C.

    Structurei

    3D structure databases

    ProteinModelPortaliQ12093.
    SMRiQ12093. Positions 29-409.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni122 – 1243Interaction with target base in tRNABy similarity
    Regioni179 – 1813Interaction with tRNABy similarity
    Regioni354 – 3552Interaction with tRNABy similarity

    Sequence similaritiesi

    Belongs to the MnmA/TRMU family.Curated

    Phylogenomic databases

    eggNOGiCOG0482.
    GeneTreeiENSGT00390000014323.
    HOGENOMiHOG000218046.
    KOiK00566.
    OMAiCAFYEGD.
    OrthoDBiEOG7034VG.

    Family and domain databases

    Gene3Di2.30.30.280. 1 hit.
    3.40.50.620. 1 hit.
    InterProiIPR023382. Adenine_a_hdrlase_dom.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR004506. tRNA-specific_2-thiouridylase.
    [Graphical view]
    PANTHERiPTHR11933. PTHR11933. 1 hit.
    PfamiPF03054. tRNA_Me_trans. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00420. trmU. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q12093-1 [UniParc]FASTAAdd to Basket

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    MLARYLNLIG RRSASPYRPQ RLPAKFDNVI VAMSSGVDSS VAAALFAGEF    50
    PNTRGVYMQN WSESQSLDDP GKEPCYERDW RDVNRVAKHL NIRVDKVNFE 100
    QDYWIDVFEP MLRGYSEGST PNPDIGCNKF VKFGKLREWL DEKYGTGNYW 150
    LVTGHYARVM QEMNGKGLFH LLRSIYRPKD QSYYLSQINS TVLSSLLLPI 200
    GHLTKPEVRD LAKYAGLPTA EKPDSQGICF VNNSQHGKFK NFLKHYLPSS 250
    PGDIITVDPQ SGAKTTWGRH DGLWSYTIGQ KVGISMPQAD PNYQGTWFVS 300
    EKLRDTNEIL IVRGRDNPAL YSDTMRIENF SSLGPREDTI NAFQNTGALT 350
    LQFRSLQVPV QIKSCKLNRS ADNLDITIHL ASKQRAITPG QSCCLYIDDR 400
    VLGSGPISHV NNNDTHA 417
    Length:417
    Mass (Da):47,049
    Last modified:November 1, 1996 - v1
    Checksum:i15BF63FD9A094890
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY624369 Genomic DNA. Translation: AAT44736.1.
    Z71781 Genomic DNA. Translation: CAA96456.1.
    Z74081 Genomic DNA. Translation: CAA98591.1.
    BK006938 Genomic DNA. Translation: DAA11820.1.
    PIRiS67566.
    RefSeqiNP_010251.1. NM_001180092.1.

    Genome annotation databases

    EnsemblFungiiYDL033C; YDL033C; YDL033C.
    GeneIDi851529.
    KEGGisce:YDL033C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY624369 Genomic DNA. Translation: AAT44736.1 .
    Z71781 Genomic DNA. Translation: CAA96456.1 .
    Z74081 Genomic DNA. Translation: CAA98591.1 .
    BK006938 Genomic DNA. Translation: DAA11820.1 .
    PIRi S67566.
    RefSeqi NP_010251.1. NM_001180092.1.

    3D structure databases

    ProteinModelPortali Q12093.
    SMRi Q12093. Positions 29-409.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32024. 150 interactions.
    IntActi Q12093. 2 interactions.
    MINTi MINT-640057.
    STRINGi 4932.YDL033C.

    Proteomic databases

    MaxQBi Q12093.
    PaxDbi Q12093.
    PeptideAtlasi Q12093.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDL033C ; YDL033C ; YDL033C .
    GeneIDi 851529.
    KEGGi sce:YDL033C.

    Organism-specific databases

    CYGDi YDL033c.
    SGDi S000002191. SLM3.

    Phylogenomic databases

    eggNOGi COG0482.
    GeneTreei ENSGT00390000014323.
    HOGENOMi HOG000218046.
    KOi K00566.
    OMAi CAFYEGD.
    OrthoDBi EOG7034VG.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29458-MONOMER.

    Miscellaneous databases

    NextBioi 968917.
    PROi Q12093.

    Gene expression databases

    Genevestigatori Q12093.

    Family and domain databases

    Gene3Di 2.30.30.280. 1 hit.
    3.40.50.620. 1 hit.
    InterProi IPR023382. Adenine_a_hdrlase_dom.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR004506. tRNA-specific_2-thiouridylase.
    [Graphical view ]
    PANTHERi PTHR11933. PTHR11933. 1 hit.
    Pfami PF03054. tRNA_Me_trans. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00420. trmU. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Mutations in MTO2 related to tRNA modification impair mitochondrial gene expression and protein synthesis in the presence of a paromomycin resistance mutation in mitochondrial 15 S rRNA."
      Yan Q., Li X., Faye G., Guan M.-X.
      J. Biol. Chem. 280:29151-29157(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION.
      Strain: ATCC 201238 / W303-1B.
    2. "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.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    5. "Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases."
      Umeda N., Suzuki T., Yukawa M., Ohya Y., Shindo H., Watanabe K., Suzuki T.
      J. Biol. Chem. 280:1613-1624(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF ASP-38.
    6. "Deletion of the MTO2 gene related to tRNA modification causes a failure in mitochondrial RNA metabolism in the yeast Saccharomyces cerevisiae."
      Wang X., Yan Q., Guan M.X.
      FEBS Lett. 581:4228-4234(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiMTU1_YEAST
    AccessioniPrimary (citable) accession number: Q12093
    Secondary accession number(s): D6VRW0, Q6IUF4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 116 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 1510 molecules/cell in log phase SD medium.1 Publication
    During the reaction, ATP is used to activate the C2 atom of U34 by adenylation. After this, the persulfide sulfur on the catalytic cysteine is transferred to the C2 atom of the wobble base (U34) of mitochondrial tRNA(Lys), tRNA(Glu) and tRNA(Gln). The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards the activated C2 atom on U34. Subsequently, a transient disulfide bond is formed between the two active site cysteine residues By similarity.By similarity

    Caution

    Was originally thought to be a 5-methylaminomethyl-2-methyltransferase involved in tRNA modification.Curated

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3