SYE_ECOLI
ID SYE_ECOLI Reviewed; 471 AA.
AC P04805;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 13-AUG-1987, sequence version 1.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=Glutamate--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00022};
DE EC=6.1.1.17 {ECO:0000255|HAMAP-Rule:MF_00022, ECO:0000269|PubMed:8218204};
DE AltName: Full=Glutamyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00022};
DE Short=GluRS {ECO:0000255|HAMAP-Rule:MF_00022};
GN Name=gltX {ECO:0000255|HAMAP-Rule:MF_00022};
GN OrderedLocusNames=b2400, JW2395;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND SUBUNIT.
RX PubMed=3015933; DOI=10.1016/s0021-9258(18)67429-0;
RA Breton R., Sanfacon H., Papayannopoulos I., Biemann K., Lapointe J.;
RT "Glutamyl-tRNA synthetase of Escherichia coli. Isolation and primary
RT structure of the gltX gene and homology with other aminoacyl-tRNA
RT synthetases.";
RL J. Biol. Chem. 261:10610-10617(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-57.
RX PubMed=2201777; DOI=10.1016/0022-2836(90)90340-r;
RA Brun V., Sanfacon H., Breton R., Lapointe J.;
RT "Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase
RT gene and a tRNA operon in Escherichia coli. Transcriptional and post-
RT transcriptional regulation of gltX, valU and alaW.";
RL J. Mol. Biol. 214:845-864(1990).
RN [6]
RP PROTEIN SEQUENCE OF 112-116, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND
RP ACTIVITY REGULATION.
RX PubMed=8218204; DOI=10.1021/bi00093a016;
RA Liu J., Lin S.-X., Blochet J.-E., Pezolet M., Lapointe J.;
RT "The glutamyl-tRNA synthetase of Escherichia coli contains one atom of zinc
RT essential for its native conformation and its catalytic activity.";
RL Biochemistry 32:11390-11396(1993).
RN [7]
RP FUNCTION.
RX PubMed=6280993;
RA Kern D., Lapointe J.;
RT "The catalytic mechanism of glutamyl-tRNA synthetase of Escherichia coli.
RT Evidence for a two-step aminoacylation pathway, and study of the reactivity
RT of the intermediate complex.";
RL Eur. J. Biochem. 106:137-150(1980).
RN [8]
RP FUNCTION.
RX PubMed=6986385; DOI=10.1016/s0021-9258(19)85976-8;
RA Kern D., Lapointe J.;
RT "The catalytic mechanism of the glutamyl-tRNA synthetase from Escherichia
RT coli. Detection of an intermediate complex in which glutamate is
RT activated.";
RL J. Biol. Chem. 255:1956-1961(1980).
RN [9]
RP FUNCTION, COFACTOR, ZINC-BINDING SITES, AND MUTAGENESIS OF CYS-98; CYS-100;
RP CYS-125; HIS-127; HIS-129; HIS-131; HIS-132 AND CYS-138.
RX PubMed=7797500; DOI=10.1074/jbc.270.25.15162;
RA Liu J., Gagnon Y., Gauthier J., Furenlid L., L'Heureux P.-J., Auger M.,
RA Nureki O., Yokoyama S., Lapointe J.;
RT "The zinc-binding site of Escherichia coli glutamyl-tRNA synthetase is
RT located in the acceptor-binding domain. Studies by extended x-ray
RT absorption fine structure, molecular modeling, and site-directed
RT mutagenesis.";
RL J. Biol. Chem. 270:15162-15169(1995).
RN [10]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [11]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF CYS-100.
RX PubMed=14764088; DOI=10.1111/j.1432-1033.2003.03976.x;
RA Banerjee R., Dubois D.Y., Gauthier J., Lin S.-X., Roy S., Lapointe J.;
RT "The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM
RT domain that modulates amino acid binding via the tRNA acceptor arm.";
RL Eur. J. Biochem. 271:724-733(2004).
RN [12]
RP FUNCTION, ACTIVITY REGULATION, PHOSPHORYLATION AT SER-239 BY HIPA, MASS
RP SPECTROMETRY, AND MUTAGENESIS OF SER-239.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=24095282; DOI=10.1016/j.molcel.2013.08.045;
RA Germain E., Castro-Roa D., Zenkin N., Gerdes K.;
RT "Molecular mechanism of bacterial persistence by HipA.";
RL Mol. Cell 52:248-254(2013).
RN [13]
RP FUNCTION, ACTIVITY REGULATION, AND PHOSPHORYLATION AT SER-239 BY HIPA.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=24343429; DOI=10.1038/ncomms4001;
RA Kaspy I., Rotem E., Weiss N., Ronin I., Balaban N.Q., Glaser G.;
RT "HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-
RT tRNA-synthetase.";
RL Nat. Commun. 4:3001-3001(2013).
RN [14]
RP FUNCTION.
RC STRAIN=B / BL21-DE3;
RX PubMed=28430938; DOI=10.1093/femsle/fnx086;
RA Maeda Y., Lin C.Y., Ishida Y., Inouye M., Yamaguchi Y., Phadtare S.;
RT "Characterization of YjjJ toxin of Escherichia coli.";
RL FEMS Microbiol. Lett. 0:0-0(2017).
CC -!- FUNCTION: Catalyzes the attachment of glutamate to tRNA(Glu) in a two-
CC step reaction: glutamate is first activated by ATP to form Glu-AMP and
CC then transferred to the acceptor end of tRNA(Glu).
CC {ECO:0000269|PubMed:14764088, ECO:0000269|PubMed:6280993,
CC ECO:0000269|PubMed:6986385, ECO:0000269|PubMed:7797500,
CC ECO:0000269|PubMed:8218204}.
CC -!- FUNCTION: Phosphorylation of GltX by HipA prevents it from being
CC charged, leading to an increase in uncharged tRNA(Glu). This induces
CC amino acid starvation and the stringent response via RelA/SpoT and
CC increased (p)ppGpp levels, which inhibits replication, transcription,
CC translation and cell wall synthesis, reducing growth and leading to
CC multidrug resistance and persistence (PubMed:24095282,
CC PubMed:24343429). Overexpression of GltX prevents HipA-induced growth
CC arrest, persister formation and increases in (p)ppGpp levels
CC (PubMed:24343429, PubMed:28430938). {ECO:0000269|PubMed:24095282,
CC ECO:0000269|PubMed:24343429, ECO:0000269|PubMed:28430938}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-
CC glutamyl-tRNA(Glu); Xref=Rhea:RHEA:23540, Rhea:RHEA-COMP:9663,
CC Rhea:RHEA-COMP:9680, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:78442, ChEBI:CHEBI:78520,
CC ChEBI:CHEBI:456215; EC=6.1.1.17; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00022, ECO:0000269|PubMed:8218204};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00022,
CC ECO:0000269|PubMed:7797500, ECO:0000269|PubMed:8218204};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00022,
CC ECO:0000269|PubMed:7797500, ECO:0000269|PubMed:8218204};
CC -!- ACTIVITY REGULATION: Inhibited by 1,10-phenanthroline (PubMed:8218204).
CC Phosphorylation of Ser-239 by HipA inhibits aminoacylation of tRNA(Glu)
CC (PubMed:24095282, PubMed:24343429). {ECO:0000269|PubMed:24095282,
CC ECO:0000269|PubMed:24343429, ECO:0000269|PubMed:8218204}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.32 uM for tRNA(Glu) {ECO:0000269|PubMed:14764088};
CC KM=0.105 mM for Glu {ECO:0000269|PubMed:14764088};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00022,
CC ECO:0000269|PubMed:3015933}.
CC -!- INTERACTION:
CC P04805; P76160: ydfR; NbExp=2; IntAct=EBI-549949, EBI-544071;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00022}.
CC -!- PTM: Phosphorylated by HipA on Ser-239 in the presence but not absence
CC of tRNA(Glu). Phosphorylated protein cannot aminoacylate tRNA(Glu).
CC {ECO:0000269|PubMed:24095282, ECO:0000269|PubMed:24343429}.
CC -!- MASS SPECTROMETRY: Mass=56224.09; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:24095282};
CC -!- MASS SPECTROMETRY: Mass=56304.11; Method=MALDI; Note=Phosphorylated.;
CC Evidence={ECO:0000269|PubMed:24095282};
CC -!- MISCELLANEOUS: This is the smallest aminoacyl-tRNA synthetase of
CC E.coli; it does not bind glutamate in the absence of cognate tRNA,
CC which is therefore required for activation of the amino acid substrate.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC Glutamate--tRNA ligase type 1 subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_00022}.
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DR EMBL; X63976; CAA45391.1; -; Genomic_DNA.
DR EMBL; M13687; AAA65715.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75457.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16272.1; -; Genomic_DNA.
DR EMBL; X55737; CAA39269.1; -; Genomic_DNA.
DR PIR; A25956; SYECET.
DR RefSeq; NP_416899.1; NC_000913.3.
DR RefSeq; WP_000695655.1; NZ_STEB01000008.1.
DR AlphaFoldDB; P04805; -.
DR SMR; P04805; -.
DR BioGRID; 4259193; 45.
DR DIP; DIP-9810N; -.
DR IntAct; P04805; 16.
DR STRING; 511145.b2400; -.
DR BindingDB; P04805; -.
DR iPTMnet; P04805; -.
DR jPOST; P04805; -.
DR PaxDb; P04805; -.
DR PRIDE; P04805; -.
DR EnsemblBacteria; AAC75457; AAC75457; b2400.
DR EnsemblBacteria; BAA16272; BAA16272; BAA16272.
DR GeneID; 66673731; -.
DR GeneID; 946906; -.
DR KEGG; ecj:JW2395; -.
DR KEGG; eco:b2400; -.
DR PATRIC; fig|1411691.4.peg.4330; -.
DR EchoBASE; EB0402; -.
DR eggNOG; COG0008; Bacteria.
DR HOGENOM; CLU_015768_6_0_6; -.
DR InParanoid; P04805; -.
DR OMA; HYINTLP; -.
DR PhylomeDB; P04805; -.
DR BioCyc; EcoCyc:GLURS-MON; -.
DR BioCyc; MetaCyc:GLURS-MON; -.
DR BRENDA; 6.1.1.17; 2026.
DR SABIO-RK; P04805; -.
DR PRO; PR:P04805; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004818; F:glutamate-tRNA ligase activity; IDA:EcoCyc.
DR GO; GO:0000049; F:tRNA binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0006424; P:glutamyl-tRNA aminoacylation; IMP:EcoCyc.
DR CDD; cd00808; GluRS_core; 1.
DR Gene3D; 1.10.10.350; -; 1.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_00022; Glu_tRNA_synth_type1; 1.
DR InterPro; IPR045462; aa-tRNA-synth_I_cd-bd.
DR InterPro; IPR020751; aa-tRNA-synth_I_codon-bd_sub2.
DR InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR InterPro; IPR008925; aa_tRNA-synth_I_cd-bd_sf.
DR InterPro; IPR004527; Glu-tRNA-ligase_bac/mito.
DR InterPro; IPR000924; Glu/Gln-tRNA-synth.
DR InterPro; IPR020058; Glu/Gln-tRNA-synth_Ib_cat-dom.
DR InterPro; IPR033910; GluRS_core.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR Pfam; PF19269; Anticodon_2; 1.
DR Pfam; PF00749; tRNA-synt_1c; 1.
DR PRINTS; PR00987; TRNASYNTHGLU.
DR SUPFAM; SSF48163; SSF48163; 1.
DR TIGRFAMs; TIGR00464; gltX_bact; 1.
DR PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
PE 1: Evidence at protein level;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Ligase; Metal-binding; Nucleotide-binding;
KW Phosphoprotein; Protein biosynthesis; Reference proteome; Zinc.
FT CHAIN 1..471
FT /note="Glutamate--tRNA ligase"
FT /id="PRO_0000119555"
FT MOTIF 9..19
FT /note="'HIGH' region"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00022"
FT MOTIF 237..241
FT /note="'KMSKS' region"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00022"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 125
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 127
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 240
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 239
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:24095282,
FT ECO:0000269|PubMed:24343429"
FT MUTAGEN 98
FT /note="C->S: 10-fold decrease in activity. Strong decrease
FT in zinc content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 100
FT /note="C->S: Loss of activity. Strong decrease in zinc
FT content."
FT /evidence="ECO:0000269|PubMed:14764088,
FT ECO:0000269|PubMed:7797500"
FT MUTAGEN 100
FT /note="C->Y: Does not prevent zinc binding. Reduces only 2-
FT fold the binding affinity for tRNA(Glu), but reduces more
FT than 10-fold the affinity for glutamate in the presence of
FT tRNA(Glu)."
FT /evidence="ECO:0000269|PubMed:14764088,
FT ECO:0000269|PubMed:7797500"
FT MUTAGEN 125
FT /note="C->S: Loss of activity. Strong decrease in zinc
FT content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 127
FT /note="H->Q: 10-fold decrease in activity. Strong decrease
FT in zinc content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 129
FT /note="H->Q: No change in activity or in zinc content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 131
FT /note="H->Q: No change in activity or in zinc content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 132
FT /note="H->Q: No change in activity or in zinc content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 138
FT /note="C->S: No change in activity or in zinc content."
FT /evidence="ECO:0000269|PubMed:7797500"
FT MUTAGEN 239
FT /note="S->D: Does not aminoacylate tRNA(Glu), not
FT phosphorylated by HipA."
FT /evidence="ECO:0000269|PubMed:24095282"
SQ SEQUENCE 471 AA; 53816 MW; 8264A799E5383398 CRC64;
MKIKTRFAPS PTGYLHVGGA RTALYSWLFA RNHGGEFVLR IEDTDLERST PEAIEAIMDG
MNWLSLEWDE GPYYQTKRFD RYNAVIDQML EEGTAYKCYC SKERLEALRE EQMAKGEKPR
YDGRCRHSHE HHADDEPCVV RFANPQEGSV VFDDQIRGPI EFSNQELDDL IIRRTDGSPT
YNFCVVVDDW DMEITHVIRG EDHINNTPRQ INILKALKAP VPVYAHVSMI NGDDGKKLSK
RHGAVSVMQY RDDGYLPEAL LNYLVRLGWS HGDQEIFTRE EMIKYFTLNA VSKSASAFNT
DKLLWLNHHY INALPPEYVA THLQWHIEQE NIDTRNGPQL ADLVKLLGER CKTLKEMAQS
CRYFYEDFAE FDADAAKKHL RPVARQPLEV VRDKLAAITD WTAENVHHAI QATADELEVG
MGKVGMPLRV AVTGAGQSPA LDVTVHAIGK TRSIERINKA LDFIAERENQ Q
