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P38088

- SYG_YEAST

UniProt

P38088 - SYG_YEAST

Protein

Glycine--tRNA ligase 1, mitochondrial

Gene

GRS1

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 131 (01 Oct 2014)
      Sequence version 3 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs By similarity.By similarity

    Catalytic activityi

    ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei132 – 1321SubstrateBy similarity
    Binding sitei251 – 2511SubstrateBy similarity
    Binding sitei388 – 3881SubstrateBy similarity
    Binding sitei388 – 3881Substrate; via carbonyl oxygenBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi283 – 2853ATPBy similarity
    Nucleotide bindingi293 – 2986ATPBy similarity
    Nucleotide bindingi410 – 4112ATPBy similarity
    Nucleotide bindingi535 – 5384ATPBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. glycine-tRNA ligase activity Source: UniProtKB
    3. protein dimerization activity Source: UniProtKB

    GO - Biological processi

    1. diadenosine tetraphosphate biosynthetic process Source: UniProtKB
    2. DNA-templated transcription, termination Source: SGD
    3. glycyl-tRNA aminoacylation Source: SGD
    4. mitochondrial glycyl-tRNA aminoacylation Source: SGD

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29078-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycine--tRNA ligase 1, mitochondrial (EC:6.1.1.14)
    Alternative name(s):
    Diadenosine tetraphosphate synthetase
    Short name:
    AP-4-A synthetase
    Glycyl-tRNA synthetase 1
    Short name:
    GlyRS 1
    Short name:
    GlyRS1
    Gene namesi
    Name:GRS1
    Ordered Locus Names:YBR121C
    ORF Names:YBR0917
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    CYGDiYBR121c.
    SGDiS000000325. GRS1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. mitochondrial matrix Source: UniProtKB-SubCell
    3. mitochondrion Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 2424MitochondrionSequence AnalysisAdd
    BLAST
    Chaini25 – 690666Glycine--tRNA ligase 1, mitochondrialPRO_0000073005Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei25 – 251N-acetylserine1 Publication
    Modified residuei226 – 2261Phosphoserine4 Publications
    Modified residuei476 – 4761Phosphoserine2 Publications
    Modified residuei528 – 5281Phosphoserine1 Publication
    Modified residuei689 – 6891Phosphothreonine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP38088.
    PaxDbiP38088.
    PeptideAtlasiP38088.
    PRIDEiP38088.

    Expressioni

    Gene expression databases

    GenevestigatoriP38088.

    Interactioni

    Subunit structurei

    Homodimer.

    Protein-protein interaction databases

    BioGridi32823. 41 interactions.
    DIPiDIP-6526N.
    IntActiP38088. 13 interactions.
    MINTiMINT-690383.
    STRINGi4932.YBR121C.

    Structurei

    3D structure databases

    ProteinModelPortaliP38088.
    SMRiP38088. Positions 39-437, 521-671.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni298 – 3025Substrate bindingBy similarity
    Regioni531 – 5355Substrate bindingBy similarity

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0423.
    HOGENOMiHOG000242015.
    KOiK01880.
    OMAiLMFQTTI.
    OrthoDBiEOG76TB17.

    Family and domain databases

    Gene3Di3.40.50.800. 1 hit.
    InterProiIPR002314. aa-tRNA-synt_IIb_cons-dom.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR027031. Gly-tRNA_synthase/POLG2.
    IPR002315. tRNA-synt_gly.
    [Graphical view]
    PANTHERiPTHR10745. PTHR10745. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01043. TRNASYNTHGLY.
    SUPFAMiSSF52954. SSF52954. 1 hit.
    TIGRFAMsiTIGR00389. glyS_dimeric. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

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

    This entry describes 2 isoformsi produced by alternative initiation. Align

    Isoform Mitochondrial (identifier: P38088-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSFFNISRRF YSQIVKKSVK IKRMSVEDIK KARAAVPFNR EQLESVLRGR    50
    FFYAPAFDLY GGVSGLYDYG PPGCAFQNNI IDAWRKHFIL EEDMLEVDCT 100
    MLTPYEVLKT SGHVDKFSDW MCRDLKTGEI FRADHLVEEV LEARLKGDQE 150
    ARGLVEDANA AAKDDAEKKK RKKKVKQIKA VKLDDDVVKE YEEILAKIDG 200
    YSGPELGELM EKYDIGNPVT GETLESPRAF NLMFETAIGP SGQLKGYLRP 250
    ETAQGQFLNF NKLLEFNNSK TPFASASIGK SFRNEISPRA GLLRVREFLM 300
    AEIEHFVDPL DKSHPKFNEI KDIKLSFLPR DVQEAGSTEP IVKTVGEAVA 350
    SRMVDNETLG YFIARIYQFL MKIGVDESKL RFRQHMANEM AHYAADCWDG 400
    ELKTSYGWIE CVGCADRSAY DLTVHSKKTK EKLVVRQKLD NPIEVTKWEI 450
    DLTKKLFGPK FRKDAPKVES HLLNMSQDDL ASKAELLKAN GKFTIKVDGV 500
    DGEVELDDKL VKIEQRTKVE HVREYVPSVI EPSFGIGRII YSVFEHSFWN 550
    RPEDNARSVL SFPPLVAPTK VLLVPLSNHK DLVPVTTEVA KILRKSQIPF 600
    KIDDSGVSIG KRYARNDELG TPFGVTIDFE SAKDHSVTLR ERDSTKQVRG 650
    SVENVIKAIR DITYNGASWE EGTKDLTPFI AQAEAEAETD 690

    Note: Produced by alternative initiation at an upstream UUG codon in-frame of the first AUG used for isoform Cytoplasmic.

    Length:690
    Mass (Da):78,184
    Last modified:July 27, 2011 - v3
    Checksum:i4EBDE6F0A942F7F6
    GO
    Isoform Cytoplasmic (identifier: P38088-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-23: Missing.

    Show »
    Length:667
    Mass (Da):75,339
    Checksum:iB62E3DDAD7E87552
    GO

    Sequence cautioni

    The sequence CAA55623.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence CAA85078.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence DAA07239.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti586 – 5872TT → HH in CAA55623. (PubMed:7900426)Curated
    Sequence conflicti586 – 5872TT → HH in CAA85078. (PubMed:7813418)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 2323Missing in isoform Cytoplasmic. CuratedVSP_041147Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X78993 Genomic DNA. Translation: CAA55623.1. Different initiation.
    Z35990 Genomic DNA. Translation: CAA85078.1. Different initiation.
    BK006936 Genomic DNA. Translation: DAA07239.2. Different initiation.
    PIRiS48285.
    RefSeqiNP_009679.2. NM_001178469.2. [P38088-2]

    Genome annotation databases

    GeneIDi852418.
    KEGGisce:YBR121C.

    Keywords - Coding sequence diversityi

    Alternative initiation

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X78993 Genomic DNA. Translation: CAA55623.1 . Different initiation.
    Z35990 Genomic DNA. Translation: CAA85078.1 . Different initiation.
    BK006936 Genomic DNA. Translation: DAA07239.2 . Different initiation.
    PIRi S48285.
    RefSeqi NP_009679.2. NM_001178469.2. [P38088-2 ]

    3D structure databases

    ProteinModelPortali P38088.
    SMRi P38088. Positions 39-437, 521-671.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32823. 41 interactions.
    DIPi DIP-6526N.
    IntActi P38088. 13 interactions.
    MINTi MINT-690383.
    STRINGi 4932.YBR121C.

    Proteomic databases

    MaxQBi P38088.
    PaxDbi P38088.
    PeptideAtlasi P38088.
    PRIDEi P38088.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 852418.
    KEGGi sce:YBR121C.

    Organism-specific databases

    CYGDi YBR121c.
    SGDi S000000325. GRS1.

    Phylogenomic databases

    eggNOGi COG0423.
    HOGENOMi HOG000242015.
    KOi K01880.
    OMAi LMFQTTI.
    OrthoDBi EOG76TB17.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29078-MONOMER.

    Miscellaneous databases

    NextBioi 971279.

    Gene expression databases

    Genevestigatori P38088.

    Family and domain databases

    Gene3Di 3.40.50.800. 1 hit.
    InterProi IPR002314. aa-tRNA-synt_IIb_cons-dom.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR027031. Gly-tRNA_synthase/POLG2.
    IPR002315. tRNA-synt_gly.
    [Graphical view ]
    PANTHERi PTHR10745. PTHR10745. 1 hit.
    Pfami PF03129. HGTP_anticodon. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view ]
    PRINTSi PR01043. TRNASYNTHGLY.
    SUPFAMi SSF52954. SSF52954. 1 hit.
    TIGRFAMsi TIGR00389. glyS_dimeric. 1 hit.
    PROSITEi PS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Analysis of a 70 kb region on the right arm of yeast chromosome II."
      Mannhaupt G., Stucka R., Ehnle S., Vetter I., Feldmann H.
      Yeast 10:1363-1381(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 586-587.
      Strain: ATCC 204508 / S288c.
    4. "One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions."
      Turner R.J., Lovato M., Schimmel P.
      J. Biol. Chem. 275:27681-27688(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. "Translation initiation from a naturally occurring non-AUG codon in Saccharomyces cerevisiae."
      Chang K.J., Wang C.C.
      J. Biol. Chem. 279:13778-13785(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: ALTERNATIVE INITIATION.
    7. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
      Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
      Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: YAL6B.
    8. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    9. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226; SER-476 AND SER-528, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-226; SER-476 AND THR-689, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-25, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSYG_YEAST
    AccessioniPrimary (citable) accession number: P38088
    Secondary accession number(s): D6VQB9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 131 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 98400 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    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 II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    External Data

    Dasty 3