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Protein

Glutamate--tRNA ligase

Gene

gltX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).
Phosphorylation of GltX by HipA prevents it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to multidrug resistance and persistence.

Catalytic activityi

ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).1 Publication

Cofactori

Zn2+2 PublicationsNote: Binds 1 zinc ion per subunit.2 Publications

Enzyme regulationi

Inhibited by 1,10-phenanthroline. Phosphorylation of Ser-239 by HipA inhibits aminoacylation of tRNA(Glu).2 Publications

Kineticsi

  1. KM=0.32 µM for tRNA(Glu)1 Publication
  2. KM=0.105 mM for Glu1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi98 – 981Zinc
    Metal bindingi100 – 1001Zinc
    Metal bindingi125 – 1251Zinc
    Metal bindingi127 – 1271Zinc
    Binding sitei240 – 2401ATPBy similarity

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-HAMAP
    • glutamate-tRNA ligase activity Source: EcoCyc
    • tRNA binding Source: InterPro
    • zinc ion binding Source: EcoCyc

    GO - Biological processi

    • glutamyl-tRNA aminoacylation Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:GLURS-MONOMER.
    ECOL316407:JW2395-MONOMER.
    MetaCyc:GLURS-MONOMER.
    BRENDAi6.1.1.17. 2026.
    SABIO-RKP04805.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glutamate--tRNA ligase (EC:6.1.1.17)
    Alternative name(s):
    Glutamyl-tRNA synthetase
    Short name:
    GluRS
    Gene namesi
    Name:gltX
    Ordered Locus Names:b2400, JW2395
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10407. gltX.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi98 – 981C → S: 10-fold decrease in activity. Strong decrease in zinc content. 1 Publication
    Mutagenesisi100 – 1001C → S: Loss of activity. Strong decrease in zinc content. 2 Publications
    Mutagenesisi100 – 1001C → Y: Does not prevent zinc binding. Reduces only 2-fold the binding affinity for tRNA(Glu), but reduces more than 10-fold the affinity for glutamate in the presence of tRNA(Glu). 2 Publications
    Mutagenesisi125 – 1251C → S: Loss of activity. Strong decrease in zinc content. 1 Publication
    Mutagenesisi127 – 1271H → Q: 10-fold decrease in activity. Strong decrease in zinc content. 1 Publication
    Mutagenesisi129 – 1291H → Q: No change in activity or in zinc content. 1 Publication
    Mutagenesisi131 – 1311H → Q: No change in activity or in zinc content. 1 Publication
    Mutagenesisi132 – 1321H → Q: No change in activity or in zinc content. 1 Publication
    Mutagenesisi138 – 1381C → S: No change in activity or in zinc content. 1 Publication
    Mutagenesisi239 – 2391S → D: Does not aminoacylate tRNA(Glu), not phosphorylated by HipA. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 471471Glutamate--tRNA ligasePRO_0000119555Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei239 – 2391Phosphoserine1 Publication

    Post-translational modificationi

    Phosphorylated by HipA on Ser-239 in the presence but not absence of tRNA(Glu). Phosphorylated protein cannot aminoacylate tRNA(Glu).1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiP04805.
    PRIDEiP04805.

    Expressioni

    Gene expression databases

    GenevestigatoriP04805.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-9810N.
    IntActiP04805. 16 interactions.
    MINTiMINT-1296746.
    STRINGi511145.b2400.

    Structurei

    3D structure databases

    ProteinModelPortaliP04805.
    SMRiP04805. Positions 3-441.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi9 – 1911"HIGH" regionAdd
    BLAST
    Motifi237 – 2415"KMSKS" region

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0008.
    HOGENOMiHOG000252722.
    InParanoidiP04805.
    KOiK01885.
    OMAiIEAFKWV.
    OrthoDBiEOG6DRPF7.
    PhylomeDBiP04805.

    Family and domain databases

    Gene3Di1.10.10.350. 1 hit.
    1.10.1160.10. 1 hit.
    3.40.50.620. 2 hits.
    HAMAPiMF_00022_B. Glu_tRNA_synth_B.
    InterProiIPR008925. aa-tRNA-synth_I_codon-bd.
    IPR020751. aa-tRNA-synth_I_codon-bd_sub2.
    IPR001412. aa-tRNA-synth_I_CS.
    IPR004527. Glu-tRNA-ligase_bac/mito.
    IPR000924. Glu/Gln-tRNA-synth.
    IPR020061. Glu/Gln-tRNA-synth_Ib_a-bdl.
    IPR020058. Glu/Gln-tRNA-synth_Ib_cat-dom.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view]
    PANTHERiPTHR10119. PTHR10119. 1 hit.
    PfamiPF00749. tRNA-synt_1c. 1 hit.
    [Graphical view]
    PRINTSiPR00987. TRNASYNTHGLU.
    SUPFAMiSSF48163. SSF48163. 1 hit.
    TIGRFAMsiTIGR00464. gltX_bact. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P04805-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKIKTRFAPS PTGYLHVGGA RTALYSWLFA RNHGGEFVLR IEDTDLERST
    60 70 80 90 100
    PEAIEAIMDG MNWLSLEWDE GPYYQTKRFD RYNAVIDQML EEGTAYKCYC
    110 120 130 140 150
    SKERLEALRE EQMAKGEKPR YDGRCRHSHE HHADDEPCVV RFANPQEGSV
    160 170 180 190 200
    VFDDQIRGPI EFSNQELDDL IIRRTDGSPT YNFCVVVDDW DMEITHVIRG
    210 220 230 240 250
    EDHINNTPRQ INILKALKAP VPVYAHVSMI NGDDGKKLSK RHGAVSVMQY
    260 270 280 290 300
    RDDGYLPEAL LNYLVRLGWS HGDQEIFTRE EMIKYFTLNA VSKSASAFNT
    310 320 330 340 350
    DKLLWLNHHY INALPPEYVA THLQWHIEQE NIDTRNGPQL ADLVKLLGER
    360 370 380 390 400
    CKTLKEMAQS CRYFYEDFAE FDADAAKKHL RPVARQPLEV VRDKLAAITD
    410 420 430 440 450
    WTAENVHHAI QATADELEVG MGKVGMPLRV AVTGAGQSPA LDVTVHAIGK
    460 470
    TRSIERINKA LDFIAERENQ Q
    Length:471
    Mass (Da):53,816
    Last modified:August 13, 1987 - v1
    Checksum:i8264A799E5383398
    GO

    Mass spectrometryi

    Molecular mass is 56224.09 Da from positions 1 - 471. Determined by MALDI. 1 Publication
    Molecular mass is 56304.11 Da from positions 1 - 471. Determined by MALDI. Phosphorylated.1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X63976 Genomic DNA. Translation: CAA45391.1.
    M13687 Genomic DNA. Translation: AAA65715.1.
    U00096 Genomic DNA. Translation: AAC75457.1.
    AP009048 Genomic DNA. Translation: BAA16272.1.
    X55737 Genomic DNA. Translation: CAA39269.1.
    PIRiA25956. SYECET.
    RefSeqiNP_416899.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC75457; AAC75457; b2400.
    BAA16272; BAA16272; BAA16272.
    GeneIDi946906.
    KEGGiecj:Y75_p2364.
    eco:b2400.
    PATRICi32120177. VBIEscCol129921_2495.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X63976 Genomic DNA. Translation: CAA45391.1.
    M13687 Genomic DNA. Translation: AAA65715.1.
    U00096 Genomic DNA. Translation: AAC75457.1.
    AP009048 Genomic DNA. Translation: BAA16272.1.
    X55737 Genomic DNA. Translation: CAA39269.1.
    PIRiA25956. SYECET.
    RefSeqiNP_416899.1. NC_000913.3.

    3D structure databases

    ProteinModelPortaliP04805.
    SMRiP04805. Positions 3-441.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9810N.
    IntActiP04805. 16 interactions.
    MINTiMINT-1296746.
    STRINGi511145.b2400.

    Chemistry

    BindingDBiP04805.

    Proteomic databases

    PaxDbiP04805.
    PRIDEiP04805.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75457; AAC75457; b2400.
    BAA16272; BAA16272; BAA16272.
    GeneIDi946906.
    KEGGiecj:Y75_p2364.
    eco:b2400.
    PATRICi32120177. VBIEscCol129921_2495.

    Organism-specific databases

    EchoBASEiEB0402.
    EcoGeneiEG10407. gltX.

    Phylogenomic databases

    eggNOGiCOG0008.
    HOGENOMiHOG000252722.
    InParanoidiP04805.
    KOiK01885.
    OMAiIEAFKWV.
    OrthoDBiEOG6DRPF7.
    PhylomeDBiP04805.

    Enzyme and pathway databases

    BioCyciEcoCyc:GLURS-MONOMER.
    ECOL316407:JW2395-MONOMER.
    MetaCyc:GLURS-MONOMER.
    BRENDAi6.1.1.17. 2026.
    SABIO-RKP04805.

    Miscellaneous databases

    PROiP04805.

    Gene expression databases

    GenevestigatoriP04805.

    Family and domain databases

    Gene3Di1.10.10.350. 1 hit.
    1.10.1160.10. 1 hit.
    3.40.50.620. 2 hits.
    HAMAPiMF_00022_B. Glu_tRNA_synth_B.
    InterProiIPR008925. aa-tRNA-synth_I_codon-bd.
    IPR020751. aa-tRNA-synth_I_codon-bd_sub2.
    IPR001412. aa-tRNA-synth_I_CS.
    IPR004527. Glu-tRNA-ligase_bac/mito.
    IPR000924. Glu/Gln-tRNA-synth.
    IPR020061. Glu/Gln-tRNA-synth_Ib_a-bdl.
    IPR020058. Glu/Gln-tRNA-synth_Ib_cat-dom.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view]
    PANTHERiPTHR10119. PTHR10119. 1 hit.
    PfamiPF00749. tRNA-synt_1c. 1 hit.
    [Graphical view]
    PRINTSiPR00987. TRNASYNTHGLU.
    SUPFAMiSSF48163. SSF48163. 1 hit.
    TIGRFAMsiTIGR00464. gltX_bact. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Glutamyl-tRNA synthetase of Escherichia coli. Isolation and primary structure of the gltX gene and homology with other aminoacyl-tRNA synthetases."
      Breton R., Sanfacon H., Papayannopoulos I., Biemann K., Lapointe J.
      J. Biol. Chem. 261:10610-10617(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBUNIT.
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase gene and a tRNA operon in Escherichia coli. Transcriptional and post-transcriptional regulation of gltX, valU and alaW."
      Brun V., Sanfacon H., Breton R., Lapointe J.
      J. Mol. Biol. 214:845-864(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-57.
    6. "The glutamyl-tRNA synthetase of Escherichia coli contains one atom of zinc essential for its native conformation and its catalytic activity."
      Liu J., Lin S.-X., Blochet J.-E., Pezolet M., Lapointe J.
      Biochemistry 32:11390-11396(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 112-116, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION.
    7. "The catalytic mechanism of glutamyl-tRNA synthetase of Escherichia coli. Evidence for a two-step aminoacylation pathway, and study of the reactivity of the intermediate complex."
      Kern D., Lapointe J.
      Eur. J. Biochem. 106:137-150(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "The catalytic mechanism of the glutamyl-tRNA synthetase from Escherichia coli. Detection of an intermediate complex in which glutamate is activated."
      Kern D., Lapointe J.
      J. Biol. Chem. 255:1956-1961(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "The zinc-binding site of Escherichia coli glutamyl-tRNA synthetase is located in the acceptor-binding domain. Studies by extended x-ray absorption fine structure, molecular modeling, and site-directed mutagenesis."
      Liu J., Gagnon Y., Gauthier J., Furenlid L., L'Heureux P.-J., Auger M., Nureki O., Yokoyama S., Lapointe J.
      J. Biol. Chem. 270:15162-15169(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, ZINC-BINDING SITES, MUTAGENESIS OF CYS-98; CYS-100; CYS-125; HIS-127; HIS-129; HIS-131; HIS-132 AND CYS-138.
    10. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    11. "The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm."
      Banerjee R., Dubois D.Y., Gauthier J., Lin S.-X., Roy S., Lapointe J.
      Eur. J. Biochem. 271:724-733(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-100.
    12. "Molecular mechanism of bacterial persistence by HipA."
      Germain E., Castro-Roa D., Zenkin N., Gerdes K.
      Mol. Cell 52:248-254(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME REGULATION, PHOSPHORYLATION BY HIPA, MASS SPECTROMETRY, MUTAGENESIS OF SER-239.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiSYE_ECOLI
    AccessioniPrimary (citable) accession number: P04805
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: August 13, 1987
    Last modified: May 27, 2015
    This is version 139 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    This is the smallest aminoacyl-tRNA synthetase of E.coli; it does not bind glutamate in the absence of cognate tRNA, which is therefore required for activation of the amino acid substrate.

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    3. SIMILARITY comments
      Index of protein domains and families

    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.