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Glutamate--tRNA ligase (EC 6.1.1.17) (Glutamyl-tRNA synthetase) (GluRS)

 SYE_ECOLI               Reviewed;         471 AA.
P04805;
13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
13-AUG-1987, sequence version 1.
25-OCT-2017, entry version 159.
RecName: Full=Glutamate--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00022};
EC=6.1.1.17 {ECO:0000255|HAMAP-Rule:MF_00022, ECO:0000269|PubMed:8218204};
AltName: Full=Glutamyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00022};
Short=GluRS {ECO:0000255|HAMAP-Rule:MF_00022};
Name=gltX {ECO:0000255|HAMAP-Rule:MF_00022};
OrderedLocusNames=b2400, JW2395;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND SUBUNIT.
PubMed=3015933;
Breton R., Sanfacon H., Papayannopoulos I., Biemann K., Lapointe J.;
"Glutamyl-tRNA synthetase of Escherichia coli. Isolation and primary
structure of the gltX gene and homology with other aminoacyl-tRNA
synthetases.";
J. Biol. Chem. 261:10610-10617(1986).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9205837; DOI=10.1093/dnares/4.2.91;
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.;
"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.";
DNA Res. 4:91-113(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-57.
PubMed=2201777; DOI=10.1016/0022-2836(90)90340-R;
Brun V., Sanfacon H., Breton R., Lapointe J.;
"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.";
J. Mol. Biol. 214:845-864(1990).
[6]
PROTEIN SEQUENCE OF 112-116, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
AND ENZYME REGULATION.
PubMed=8218204; DOI=10.1021/bi00093a016;
Liu J., Lin S.-X., Blochet J.-E., Pezolet M., Lapointe J.;
"The glutamyl-tRNA synthetase of Escherichia coli contains one atom of
zinc essential for its native conformation and its catalytic
activity.";
Biochemistry 32:11390-11396(1993).
[7]
FUNCTION.
PubMed=6280993;
Kern D., Lapointe J.;
"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.";
Eur. J. Biochem. 106:137-150(1980).
[8]
FUNCTION.
PubMed=6986385;
Kern D., Lapointe J.;
"The catalytic mechanism of the glutamyl-tRNA synthetase from
Escherichia coli. Detection of an intermediate complex in which
glutamate is activated.";
J. Biol. Chem. 255:1956-1961(1980).
[9]
FUNCTION, COFACTOR, ZINC-BINDING SITES, AND MUTAGENESIS OF CYS-98;
CYS-100; CYS-125; HIS-127; HIS-129; HIS-131; HIS-132 AND CYS-138.
PubMed=7797500; DOI=10.1074/jbc.270.25.15162;
Liu J., Gagnon Y., Gauthier J., Furenlid L., L'Heureux P.-J.,
Auger M., Nureki O., Yokoyama S., Lapointe J.;
"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.";
J. Biol. Chem. 270:15162-15169(1995).
[10]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[11]
FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF CYS-100.
PubMed=14764088; DOI=10.1111/j.1432-1033.2003.03976.x;
Banerjee R., Dubois D.Y., Gauthier J., Lin S.-X., Roy S., Lapointe J.;
"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.";
Eur. J. Biochem. 271:724-733(2004).
[12]
FUNCTION, ENZYME REGULATION, PHOSPHORYLATION AT SER-239 BY HIPA, MASS
SPECTROMETRY, AND MUTAGENESIS OF SER-239.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=24095282; DOI=10.1016/j.molcel.2013.08.045;
Germain E., Castro-Roa D., Zenkin N., Gerdes K.;
"Molecular mechanism of bacterial persistence by HipA.";
Mol. Cell 52:248-254(2013).
[13]
FUNCTION, ENZYME REGULATION, AND PHOSPHORYLATION AT SER-239 BY HIPA.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=24343429; DOI=10.1038/ncomms4001;
Kaspy I., Rotem E., Weiss N., Ronin I., Balaban N.Q., Glaser G.;
"HipA-mediated antibiotic persistence via phosphorylation of the
glutamyl-tRNA-synthetase.";
Nat. Commun. 4:3001-3001(2013).
[14]
FUNCTION.
STRAIN=B / BL21-DE3;
PubMed=28430938; DOI=10.1093/femsle/fnx086;
Maeda Y., Lin C.Y., Ishida Y., Inouye M., Yamaguchi Y., Phadtare S.;
"Characterization of YjjJ toxin of Escherichia coli.";
FEMS Microbiol. Lett. 0:0-0(2017).
-!- FUNCTION: 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).
{ECO:0000269|PubMed:14764088, ECO:0000269|PubMed:6280993,
ECO:0000269|PubMed:6986385, ECO:0000269|PubMed:7797500,
ECO:0000269|PubMed:8218204}.
-!- FUNCTION: 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 (p)ppGpp levels, which inhibits
replication, transcription, translation and cell wall synthesis,
reducing growth and leading to multidrug resistance and
persistence (PubMed:24095282, PubMed:24343429). Overexpression of
GltX prevents HipA-induced growth arrest, persister formation and
increases in (p)ppGpp levels (PubMed:24343429, PubMed:28430938).
{ECO:0000269|PubMed:24095282, ECO:0000269|PubMed:24343429,
ECO:0000269|PubMed:28430938}.
-!- CATALYTIC ACTIVITY: ATP + L-glutamate + tRNA(Glu) = AMP +
diphosphate + L-glutamyl-tRNA(Glu). {ECO:0000255|HAMAP-
Rule:MF_00022, ECO:0000269|PubMed:8218204}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000255|HAMAP-Rule:MF_00022,
ECO:0000269|PubMed:7797500, ECO:0000269|PubMed:8218204};
Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-
Rule:MF_00022, ECO:0000269|PubMed:7797500,
ECO:0000269|PubMed:8218204};
-!- ENZYME REGULATION: Inhibited by 1,10-phenanthroline
(PubMed:8218204). Phosphorylation of Ser-239 by HipA inhibits
aminoacylation of tRNA(Glu) (PubMed:24095282, PubMed:24343429).
{ECO:0000269|PubMed:24095282, ECO:0000269|PubMed:24343429,
ECO:0000269|PubMed:8218204}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.32 uM for tRNA(Glu) {ECO:0000269|PubMed:14764088};
KM=0.105 mM for Glu {ECO:0000269|PubMed:14764088};
-!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00022,
ECO:0000269|PubMed:3015933}.
-!- INTERACTION:
P76160:ydfR; NbExp=2; IntAct=EBI-549949, EBI-544071;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00022}.
-!- PTM: Phosphorylated by HipA on Ser-239 in the presence but not
absence of tRNA(Glu). Phosphorylated protein cannot aminoacylate
tRNA(Glu). {ECO:0000269|PubMed:24095282,
ECO:0000269|PubMed:24343429}.
-!- MASS SPECTROMETRY: Mass=56224.09; Method=MALDI; Range=1-471;
Evidence={ECO:0000269|PubMed:24095282};
-!- MASS SPECTROMETRY: Mass=56304.11; Method=MALDI; Range=1-471;
Note=Phosphorylated.; Evidence={ECO:0000269|PubMed:24095282};
-!- 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.
-!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase
family. Glutamate--tRNA ligase type 1 subfamily.
{ECO:0000255|HAMAP-Rule:MF_00022}.
-----------------------------------------------------------------------
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EMBL; X63976; CAA45391.1; -; Genomic_DNA.
EMBL; M13687; AAA65715.1; -; Genomic_DNA.
EMBL; U00096; AAC75457.1; -; Genomic_DNA.
EMBL; AP009048; BAA16272.1; -; Genomic_DNA.
EMBL; X55737; CAA39269.1; -; Genomic_DNA.
PIR; A25956; SYECET.
RefSeq; NP_416899.1; NC_000913.3.
RefSeq; WP_000695655.1; NZ_LN832404.1.
ProteinModelPortal; P04805; -.
SMR; P04805; -.
BioGrid; 4259193; 14.
DIP; DIP-9810N; -.
IntAct; P04805; 16.
MINT; MINT-1296746; -.
STRING; 316385.ECDH10B_2564; -.
BindingDB; P04805; -.
iPTMnet; P04805; -.
PaxDb; P04805; -.
PRIDE; P04805; -.
EnsemblBacteria; AAC75457; AAC75457; b2400.
EnsemblBacteria; BAA16272; BAA16272; BAA16272.
GeneID; 946906; -.
KEGG; ecj:JW2395; -.
KEGG; eco:b2400; -.
PATRIC; fig|1411691.4.peg.4330; -.
EchoBASE; EB0402; -.
EcoGene; EG10407; gltX.
eggNOG; ENOG4105C20; Bacteria.
eggNOG; COG0008; LUCA.
HOGENOM; HOG000252722; -.
InParanoid; P04805; -.
KO; K01885; -.
PhylomeDB; P04805; -.
BioCyc; EcoCyc:GLURS-MONOMER; -.
BioCyc; MetaCyc:GLURS-MONOMER; -.
BRENDA; 6.1.1.17; 2026.
SABIO-RK; P04805; -.
PRO; PR:P04805; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004818; F:glutamate-tRNA ligase activity; IDA:EcoCyc.
GO; GO:0000049; F:tRNA binding; IEA:InterPro.
GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
GO; GO:0006424; P:glutamyl-tRNA aminoacylation; IMP:EcoCyc.
CDD; cd00808; GluRS_core; 1.
Gene3D; 1.10.10.350; -; 1.
Gene3D; 1.10.1160.10; -; 1.
Gene3D; 1.10.8.70; -; 1.
Gene3D; 3.40.50.620; -; 2.
HAMAP; MF_00022; Glu_tRNA_synth_type1; 1.
InterPro; IPR008925; aa-tRNA-synth_I_codon-bd.
InterPro; IPR020752; aa-tRNA-synth_I_codon-bd_sub1.
InterPro; IPR020751; aa-tRNA-synth_I_codon-bd_sub2.
InterPro; IPR001412; aa-tRNA-synth_I_CS.
InterPro; IPR004527; Glu-tRNA-ligase_bac/mito.
InterPro; IPR000924; Glu/Gln-tRNA-synth.
InterPro; IPR020061; Glu/Gln-tRNA-synth_Ib_a-bdl.
InterPro; IPR020058; Glu/Gln-tRNA-synth_Ib_cat-dom.
InterPro; IPR033910; GluRS_core.
InterPro; IPR014729; Rossmann-like_a/b/a_fold.
Pfam; PF00749; tRNA-synt_1c; 1.
PRINTS; PR00987; TRNASYNTHGLU.
SUPFAM; SSF48163; SSF48163; 1.
TIGRFAMs; TIGR00464; gltX_bact; 1.
PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
1: Evidence at protein level;
Aminoacyl-tRNA synthetase; ATP-binding; Complete proteome; Cytoplasm;
Direct protein sequencing; Ligase; Metal-binding; Nucleotide-binding;
Phosphoprotein; Protein biosynthesis; Reference proteome; Zinc.
CHAIN 1 471 Glutamate--tRNA ligase.
/FTId=PRO_0000119555.
MOTIF 9 19 "HIGH" region. {ECO:0000255|HAMAP-
Rule:MF_00022}.
MOTIF 237 241 "KMSKS" region. {ECO:0000255|HAMAP-
Rule:MF_00022}.
METAL 98 98 Zinc.
METAL 100 100 Zinc.
METAL 125 125 Zinc.
METAL 127 127 Zinc.
BINDING 240 240 ATP. {ECO:0000250}.
MOD_RES 239 239 Phosphoserine.
{ECO:0000269|PubMed:24095282,
ECO:0000269|PubMed:24343429}.
MUTAGEN 98 98 C->S: 10-fold decrease in activity.
Strong decrease in zinc content.
{ECO:0000269|PubMed:7797500}.
MUTAGEN 100 100 C->S: Loss of activity. Strong decrease
in zinc content.
{ECO:0000269|PubMed:14764088,
ECO:0000269|PubMed:7797500}.
MUTAGEN 100 100 C->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).
{ECO:0000269|PubMed:14764088,
ECO:0000269|PubMed:7797500}.
MUTAGEN 125 125 C->S: Loss of activity. Strong decrease
in zinc content.
{ECO:0000269|PubMed:7797500}.
MUTAGEN 127 127 H->Q: 10-fold decrease in activity.
Strong decrease in zinc content.
{ECO:0000269|PubMed:7797500}.
MUTAGEN 129 129 H->Q: No change in activity or in zinc
content. {ECO:0000269|PubMed:7797500}.
MUTAGEN 131 131 H->Q: No change in activity or in zinc
content. {ECO:0000269|PubMed:7797500}.
MUTAGEN 132 132 H->Q: No change in activity or in zinc
content. {ECO:0000269|PubMed:7797500}.
MUTAGEN 138 138 C->S: No change in activity or in zinc
content. {ECO:0000269|PubMed:7797500}.
MUTAGEN 239 239 S->D: Does not aminoacylate tRNA(Glu),
not phosphorylated by HipA.
{ECO:0000269|PubMed:24095282}.
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


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