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Q12093

- MTU1_YEAST

UniProt

Q12093 - MTU1_YEAST

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Protein

Mitochondrial tRNA-specific 2-thiouridylase 1

Gene
SLM3, MTO2, MTU1, YDL033C, D2761
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 oxygen By similarity
Active sitei127 – 1271Nucleophile By similarity
Binding sitei154 – 1541ATP; via amide nitrogen By similarity
Sitei155 – 1551Interaction with tRNA By similarity
Active sitei229 – 2291Cysteine persulfide intermediate By similarity
Sitei281 – 2811Interaction with tRNA By similarity
Sitei391 – 3911Interaction with tRNA By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi32 – 398ATP By 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
Complete GO annotation...

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
Complete GO annotation...

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 ↔ 229Alternate By 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.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the MnmA/TRMU family.

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

« Hide

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

« Hide 'large scale' publications
  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: May 14, 2014
This is version 115 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.
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.

Caution

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

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

Similar proteinsi