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Protein

Mitochondrial tRNA-specific 2-thiouridylase 1

Gene

SLM3

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

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

  • ATP binding Source: UniProtKB-KW
  • sulfurtransferase activity Source: InterPro
  • tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity Source: SGD
  • tRNA binding Source: UniProtKB-KW

GO - Biological processi

  • mitochondrial tRNA thio-modification Source: SGD
  • 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 Componenti: Chromosome IV

Organism-specific databases

CYGDiYDL033c.
EuPathDBiFungiDB:YDL033C.
SGDiS000002191. SLM3.

Subcellular locationi

GO - Cellular componenti

  • 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 ↔ 229AlternateBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiQ12093.
PaxDbiQ12093.
PeptideAtlasiQ12093.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi32024. 152 interactions.
IntActiQ12093. 2 interactions.
MINTiMINT-640057.

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.
InParanoidiQ12093.
KOiK00566.
OMAiPIYRVDF.
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

        10         20         30         40         50
MLARYLNLIG RRSASPYRPQ RLPAKFDNVI VAMSSGVDSS VAAALFAGEF
60 70 80 90 100
PNTRGVYMQN WSESQSLDDP GKEPCYERDW RDVNRVAKHL NIRVDKVNFE
110 120 130 140 150
QDYWIDVFEP MLRGYSEGST PNPDIGCNKF VKFGKLREWL DEKYGTGNYW
160 170 180 190 200
LVTGHYARVM QEMNGKGLFH LLRSIYRPKD QSYYLSQINS TVLSSLLLPI
210 220 230 240 250
GHLTKPEVRD LAKYAGLPTA EKPDSQGICF VNNSQHGKFK NFLKHYLPSS
260 270 280 290 300
PGDIITVDPQ SGAKTTWGRH DGLWSYTIGQ KVGISMPQAD PNYQGTWFVS
310 320 330 340 350
EKLRDTNEIL IVRGRDNPAL YSDTMRIENF SSLGPREDTI NAFQNTGALT
360 370 380 390 400
LQFRSLQVPV QIKSCKLNRS ADNLDITIHL ASKQRAITPG QSCCLYIDDR
410
VLGSGPISHV NNNDTHA
Length:417
Mass (Da):47,049
Last modified:November 1, 1996 - v1
Checksum:i15BF63FD9A094890
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

BioGridi32024. 152 interactions.
IntActiQ12093. 2 interactions.
MINTiMINT-640057.

Proteomic databases

MaxQBiQ12093.
PaxDbiQ12093.
PeptideAtlasiQ12093.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYDL033c.
EuPathDBiFungiDB:YDL033C.
SGDiS000002191. SLM3.

Phylogenomic databases

eggNOGiCOG0482.
GeneTreeiENSGT00390000014323.
HOGENOMiHOG000218046.
InParanoidiQ12093.
KOiK00566.
OMAiPIYRVDF.
OrthoDBiEOG7034VG.

Enzyme and pathway databases

BioCyciYEAST:G3O-29458-MONOMER.

Miscellaneous databases

NextBioi968917.
PROiQ12093.

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.
ProtoNetiSearch...

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: July 22, 2015
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 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

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 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.