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Protein

Methionine--tRNA ligase, cytoplasmic

Gene

MES1

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 attachment of methionine to tRNA(Met) in a two-step reaction: methionine is first activated by ATP to form Met-AMP and then transferred to the acceptor end of tRNA(Met).1 Publication

Catalytic activityi

ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).3 Publications

Kineticsi

The presence of ARC1 reduces the KM for tRNA(Met) to less than 0.1 µM and increases the catalytic efficiency more than 500-fold.

  1. KM=6.6 µM for tRNA(Met) (in the absence of ARC1)3 Publications
  2. KM=10 µM for methionine3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei411 – 4111ATPBy similarity

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • methionine-tRNA ligase activity Source: SGD

    GO - Biological processi

    • methionyl-tRNA aminoacylation Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30933-MONOMER.
    BRENDAi6.1.1.10. 984.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Methionine--tRNA ligase, cytoplasmic (EC:6.1.1.10)
    Alternative name(s):
    Methionyl-tRNA synthetase
    Short name:
    MetRS
    Gene namesi
    Name:MES1
    Ordered Locus Names:YGR264C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311 Componenti: Chromosome VII

    Organism-specific databases

    EuPathDBiFungiDB:YGR264C.
    SGDiS000003496. MES1.

    Subcellular locationi

    • Cytoplasm 1 Publication

    • Note: Largely excluded from the nucleus.

    GO - Cellular componenti

    • cytoplasm Source: SGD
    • methionyl glutamyl tRNA synthetase complex Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi63 – 631A → H: Abolishes interaction with ARC1. 1 Publication
    Mutagenesisi502 – 5021G → D in mes1; renders the protein unstable in vitro, elevates the KM for methionine in vivo. 1 Publication
    Mutagenesisi584 – 5841N → D or Q: Abolishes aminoacylation activity. 1 Publication
    Mutagenesisi588 – 5881R → A, K or Q: Abolishes aminoacylation activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 751750Methionine--tRNA ligase, cytoplasmicPRO_0000139269Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine2 Publications

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP00958.
    PaxDbiP00958.
    PeptideAtlasiP00958.

    Expressioni

    Gene expression databases

    GenevestigatoriP00958.

    Interactioni

    Subunit structurei

    Component of a yeast aminoacyl-tRNA synthase (aaRS) complex formed by methionyl-tRNA synthase MES1, glutamyl-tRNA synthase GUS1 and the tRNA aminoacylation cofactor ARC1 in a stoichiometric complex. Interacts (via N-ter) with ARC1 (via N-ter). Can also form a stable binary complex with ARC1 that is functional in terms of aminoacylation. ARC1 increases the affinity for cognate tRNAs due to the presence of a tRNA binding domain in the middle and C-terminal part of ARC1.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ARC1P466727EBI-18762,EBI-7224

    Protein-protein interaction databases

    BioGridi33515. 39 interactions.
    DIPiDIP-2211N.
    IntActiP00958. 10 interactions.
    MINTiMINT-648422.
    STRINGi4932.YGR264C.

    Structurei

    Secondary structure

    1
    751
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 53Combined sources
    Beta strandi10 – 123Combined sources
    Helixi15 – 3117Combined sources
    Beta strandi49 – 513Combined sources
    Helixi61 – 688Combined sources
    Turni73 – 764Combined sources
    Helixi78 – 869Combined sources
    Turni87 – 893Combined sources
    Helixi90 – 923Combined sources
    Beta strandi93 – 953Combined sources
    Helixi98 – 11114Combined sources
    Helixi122 – 14221Combined sources
    Helixi148 – 15710Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2HSNX-ray2.20A2-160[»]
    ProteinModelPortaliP00958.
    SMRiP00958. Positions 1-160, 199-739.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00958.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni36 – 9257Interaction with ARC1Add
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi205 – 21511"HIGH" regionAdd
    BLAST
    Motifi525 – 5295"KMSKS" region

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0143.
    GeneTreeiENSGT00550000075017.
    HOGENOMiHOG000200402.
    InParanoidiP00958.
    KOiK01874.
    OMAiVEGRRNV.
    OrthoDBiEOG7CG77Z.

    Family and domain databases

    Gene3Di1.10.730.10. 1 hit.
    2.20.28.20. 1 hit.
    3.40.50.620. 2 hits.
    HAMAPiMF_00098. Met_tRNA_synth_type1.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR018285. Met-tRNA-synth_N.
    IPR023458. Met-tRNA_ligase_1.
    IPR014758. Met-tRNA_synth.
    IPR015413. Methionyl/Leucyl_tRNA_Synth.
    IPR029038. MetRS_Zn.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR009080. tRNAsynth_1a_anticodon-bd.
    [Graphical view]
    PfamiPF09635. MetRS-N. 1 hit.
    PF09334. tRNA-synt_1g. 1 hit.
    [Graphical view]
    PRINTSiPR01041. TRNASYNTHMET.
    SUPFAMiSSF47323. SSF47323. 1 hit.
    SSF57770. SSF57770. 1 hit.
    TIGRFAMsiTIGR00398. metG. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P00958-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSFLISFDKS KKHPAHLQLA NNLKIALALE YASKNLKPEV DNDNAAMELR
    60 70 80 90 100
    NTKEPFLLFD ANAILRYVMD DFEGQTSDKY QFALASLQNL LYHKELPQQH
    110 120 130 140 150
    VEVLTNKAIE NYLVELKEPL TTTDLILFAN VYALNSSLVH SKFPELPSKV
    160 170 180 190 200
    HNAVALAKKH VPRDSSSFKN IGAVKIQADL TVKPKDSEIL PKPNERNILI
    210 220 230 240 250
    TSALPYVNNV PHLGNIIGSV LSADIFARYC KGRNYNALFI CGTDEYGTAT
    260 270 280 290 300
    ETKALEEGVT PRQLCDKYHK IHSDVYKWFQ IGFDYFGRTT TDKQTEIAQH
    310 320 330 340 350
    IFTKLNSNGY LEEQSMKQLY CPVHNSYLAD RYVEGECPKC HYDDARGDQC
    360 370 380 390 400
    DKCGALLDPF ELINPRCKLD DASPEPKYSD HIFLSLDKLE SQISEWVEKA
    410 420 430 440 450
    SEEGNWSKNS KTITQSWLKD GLKPRCITRD LVWGTPVPLE KYKDKVLYVW
    460 470 480 490 500
    FDATIGYVSI TSNYTKEWKQ WWNNPEHVSL YQFMGKDNVP FHTVVFPGSQ
    510 520 530 540 550
    LGTEENWTML HHLNTTEYLQ YENGKFSKSR GVGVFGNNAQ DSGISPSVWR
    560 570 580 590 600
    YYLASVRPES SDSHFSWDDF VARNNSELLA NLGNFVNRLI KFVNAKYNGV
    610 620 630 640 650
    VPKFDPKKVS NYDGLVKDIN EILSNYVKEM ELGHERRGLE IAMSLSARGN
    660 670 680 690 700
    QFLQENKLDN TLFSQSPEKS DAVVAVGLNI IYAVSSIITP YMPEIGEKIN
    710 720 730 740 750
    KMLNAPALKI DDRFHLAILE GHNINKAEYL FQRIDEKKID EWRAKYGGQQ

    V
    Length:751
    Mass (Da):85,678
    Last modified:January 23, 2007 - v4
    Checksum:i11679C1AB8BB5E39
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti122 – 1221T → A in CAA24627 (PubMed:6341994).Curated
    Sequence conflicti122 – 1221T → A (PubMed:3905796).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    V01316 Genomic DNA. Translation: CAA24627.1.
    Y07777 Genomic DNA. Translation: CAA69086.1.
    Z73049 Genomic DNA. Translation: CAA97293.1.
    BK006941 Genomic DNA. Translation: DAA08354.1.
    PIRiS64597. SYBYMT.
    RefSeqiNP_011780.3. NM_001181393.3.

    Genome annotation databases

    EnsemblFungiiYGR264C; YGR264C; YGR264C.
    GeneIDi853181.
    KEGGisce:YGR264C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    V01316 Genomic DNA. Translation: CAA24627.1.
    Y07777 Genomic DNA. Translation: CAA69086.1.
    Z73049 Genomic DNA. Translation: CAA97293.1.
    BK006941 Genomic DNA. Translation: DAA08354.1.
    PIRiS64597. SYBYMT.
    RefSeqiNP_011780.3. NM_001181393.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2HSNX-ray2.20A2-160[»]
    ProteinModelPortaliP00958.
    SMRiP00958. Positions 1-160, 199-739.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33515. 39 interactions.
    DIPiDIP-2211N.
    IntActiP00958. 10 interactions.
    MINTiMINT-648422.
    STRINGi4932.YGR264C.

    Proteomic databases

    MaxQBiP00958.
    PaxDbiP00958.
    PeptideAtlasiP00958.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYGR264C; YGR264C; YGR264C.
    GeneIDi853181.
    KEGGisce:YGR264C.

    Organism-specific databases

    EuPathDBiFungiDB:YGR264C.
    SGDiS000003496. MES1.

    Phylogenomic databases

    eggNOGiCOG0143.
    GeneTreeiENSGT00550000075017.
    HOGENOMiHOG000200402.
    InParanoidiP00958.
    KOiK01874.
    OMAiVEGRRNV.
    OrthoDBiEOG7CG77Z.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30933-MONOMER.
    BRENDAi6.1.1.10. 984.

    Miscellaneous databases

    EvolutionaryTraceiP00958.
    NextBioi973317.
    PROiP00958.

    Gene expression databases

    GenevestigatoriP00958.

    Family and domain databases

    Gene3Di1.10.730.10. 1 hit.
    2.20.28.20. 1 hit.
    3.40.50.620. 2 hits.
    HAMAPiMF_00098. Met_tRNA_synth_type1.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR018285. Met-tRNA-synth_N.
    IPR023458. Met-tRNA_ligase_1.
    IPR014758. Met-tRNA_synth.
    IPR015413. Methionyl/Leucyl_tRNA_Synth.
    IPR029038. MetRS_Zn.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR009080. tRNAsynth_1a_anticodon-bd.
    [Graphical view]
    PfamiPF09635. MetRS-N. 1 hit.
    PF09334. tRNA-synt_1g. 1 hit.
    [Graphical view]
    PRINTSiPR01041. TRNASYNTHMET.
    SUPFAMiSSF47323. SSF47323. 1 hit.
    SSF57770. SSF57770. 1 hit.
    TIGRFAMsiTIGR00398. metG. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Primary structure of the Saccharomyces cerevisiae gene for methionyl-tRNA synthetase."
      Walter P., Gangloff J., Bonnet J., Boulanger Y., Ebel J.-P., Fasiolo F.
      Proc. Natl. Acad. Sci. U.S.A. 80:2437-2441(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Fasiolo F.
      Submitted (SEP-1983) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION.
    3. "Cytoplasmic methionyl-tRNA synthetase from Bakers' yeast. A monomer with a post-translationally modified N-terminus."
      Fasiolo F., Gibson B.W., Walter P., Chatton B., Biemann K., Boulanger Y.
      J. Biol. Chem. 260:15571-15576(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2.
    4. "Analysis of an 11.6 kb region from the right arm of chromosome VII of Saccharomyces cerevisiae between the RAD2 and the MES1 genes reveals the presence of three new genes."
      Clemente M.L., Sartori G., Cardazzo B., Carignani G.
      Yeast 13:287-290(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    5. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    7. "Strategy for the mass spectrometric verification and correction of the primary structures of proteins deduced from their DNA sequences."
      Gibson B.W., Biemann K.
      Proc. Natl. Acad. Sci. U.S.A. 81:1956-1960(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 10-90, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2.
    8. "Cloning and characterization of the yeast methionyl-tRNA synthetase mutation mes1."
      Chatton B., Winsor B., Boulanger Y., Fasiolo F.
      J. Biol. Chem. 262:15094-15097(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLY-502.
    9. "Identification of potential amino acid residues supporting anticodon recognition in yeast methionyl-tRNA synthetase."
      Despons L., Walter P., Senger B., Ebel J.-P., Fasiolo F.
      FEBS Lett. 289:217-220(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASN-584 AND ARG-588.
    10. "The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases."
      Simos G., Segref A., Fasiolo F., Hellmuth K., Shevshenko A., Mann M., Hurt E.C.
      EMBO J. 15:5437-5448(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH ARC1.
    11. "A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases."
      Simos G., Sauer A., Fasiolo F., Hurt E.C.
      Mol. Cell 1:235-242(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH ARC1.
    12. "The intracellular location of two aminoacyl-tRNA synthetases depends on complex formation with Arc1p."
      Galani K., Grosshans H., Deinert K., Hurt E.C., Simos G.
      EMBO J. 20:6889-6898(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, INTERACTION WITH ARC1, SUBCELLULAR LOCATION.
    13. "Arc1p organizes the yeast aminoacyl-tRNA synthetase complex and stabilizes its interaction with the cognate tRNAs."
      Deinert K., Fasiolo F., Hurt E.C., Simos G.
      J. Biol. Chem. 276:6000-6008(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    14. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    15. "Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes."
      Simader H., Hothorn M., Koehler C., Basquin J., Simos G., Suck D.
      Nucleic Acids Res. 34:3968-3979(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 2-160 IN COMPLEX WITH ARC1, MUTAGENESIS OF ALA-63.

    Entry informationi

    Entry nameiSYMC_YEAST
    AccessioniPrimary (citable) accession number: P00958
    Secondary accession number(s): D6VV43
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: May 27, 2015
    This is version 154 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 85000 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: 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.