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Literature summary for 4.1.1.15 extracted from

  • De Biase, D.; Pennacchietti, E.
    Glutamate decarboxylase-dependent acid resistance in orally acquired bacteria: function, distribution and biomedical implications of the gadBC operon (2012), Mol. Microbiol., 86, 770-786.
    View publication on PubMed

Crystallization (Commentary)

Crystallization (Comment) Organism
enzyme hexamer X-ray diffraction structure determination and analysis at pH 4.6 and pH 7.6 Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Cl- acts as positive allosteric modulators of GadB Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
L-glutamate Escherichia coli
-
4-aminobutanoate + CO2
-
?
L-glutamate Listeria monocytogenes
-
4-aminobutanoate + CO2
-
?
L-glutamate Levilactobacillus brevis
-
4-aminobutanoate + CO2
-
?
L-glutamate Levilactobacillus brevis ATCC 367
-
4-aminobutanoate + CO2
-
?
L-glutamate Levilactobacillus brevis FO12005
-
4-aminobutanoate + CO2
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
gene gadB
-
Levilactobacillus brevis A9ZM78 single gene gadB
-
Levilactobacillus brevis Q03U69 LVIS_0079; gene gadB
-
Levilactobacillus brevis ATCC 367 Q03U69 LVIS_0079; gene gadB
-
Levilactobacillus brevis FO12005 A9ZM78 single gene gadB
-
Listeria monocytogenes
-
gene gadB
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
L-glutamate
-
Escherichia coli 4-aminobutanoate + CO2
-
?
L-glutamate
-
Listeria monocytogenes 4-aminobutanoate + CO2
-
?
L-glutamate
-
Levilactobacillus brevis 4-aminobutanoate + CO2
-
?
L-glutamate the alpha-carboxyl group, leaving as CO2, is replaced by a cytoplasmic proton, yielding 4-aminobutanoate Listeria monocytogenes 4-aminobutanoate + CO2
-
?
L-glutamate the alpha-carboxyl group, leaving as CO2, is replaced by a cytoplasmic proton, yielding 4-aminobutanoate Levilactobacillus brevis 4-aminobutanoate + CO2
-
?
L-glutamate the alpha-carboxyl group, leaving as CO2, is thus replaced by a cytoplasmic proton, yielding 4-aminobutanoate Escherichia coli 4-aminobutanoate + CO2
-
?
L-glutamate the alpha-carboxyl group, leaving as CO2, is thus replaced by a cytoplasmic proton, yielding 4-aminobutanoate Levilactobacillus brevis 4-aminobutanoate + CO2
-
?
L-glutamate
-
Levilactobacillus brevis ATCC 367 4-aminobutanoate + CO2
-
?
L-glutamate the alpha-carboxyl group, leaving as CO2, is thus replaced by a cytoplasmic proton, yielding 4-aminobutanoate Levilactobacillus brevis ATCC 367 4-aminobutanoate + CO2
-
?
L-glutamate
-
Levilactobacillus brevis FO12005 4-aminobutanoate + CO2
-
?
L-glutamate the alpha-carboxyl group, leaving as CO2, is replaced by a cytoplasmic proton, yielding 4-aminobutanoate Levilactobacillus brevis FO12005 4-aminobutanoate + CO2
-
?

Subunits

Subunits Comment Organism
hexamer GadB is a trimer of dimers, in which monomers from each dimer belong to different layers, structure comparisons, overview Escherichia coli
tetramer Lactobacillus brevis IFO12005 is dimeric in the inactive form and tetrameric in the active form Levilactobacillus brevis

Synonyms

Synonyms Comment Organism
GadB
-
Escherichia coli
GadB
-
Listeria monocytogenes
GadB
-
Levilactobacillus brevis

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate dependent on Escherichia coli
pyridoxal 5'-phosphate dependent on Listeria monocytogenes
pyridoxal 5'-phosphate dependent on Levilactobacillus brevis

Expression

Organism Comment Expression
Escherichia coli expression of the gadBC operon increases under conditions of respiratory stress up

General Information

General Information Comment Organism
evolution clustal X-generated dendrogram of bacterial glutamate decarboxylases, overview Escherichia coli
evolution clustal X-generated dendrogram of bacterial glutamate decarboxylases, overview Listeria monocytogenes
evolution clustal X-generated dendrogram of bacterial glutamate decarboxylases, overview Levilactobacillus brevis
additional information absence of a His residue near the C-terminus in Lactobacillus brevis GadB homologue LVIS_0079 Levilactobacillus brevis
additional information at neutral pH the enzyme is in a compact conformation with access to the active site precluded by steric hindrance of some structural elements, a sequence of events lead to the conversion of GadB from the inactive into the active form and vice versa, structural determinants responsible for pH-dependent intracellular activation of GadB, overview. In its inactive form GadB has (i) the N-terminal residues 1-14 of each subunit mainly involved in dimerization and hexamerization, (ii) the C-terminal residues 452-466 ordered and protruding into the active site (with residues His465 and Thr466), like a plug, thus occupying the binding site of the physiological substrate glutamate, (iii) the beta-hairpin 300-313 contacting the C-terminal tail of the other subunit in the dimer as to hold it in place, structure comparisons, overview Escherichia coli
physiological function the glutamate-dependent acid resistance (GDAR) system is by far the most potent acid resistance system in commensal and pathogenic Escherichia coli and requires the activity of intracellular glutamate decarboxylase GadB performing a proton-consuming decarboxylation reaction and the cognate antiporter GadC, which performs the glutamate/in/gamma-aminobutyrate/out electrogenic antiport, overview Escherichia coli
physiological function the glutamate-dependent acid resistance (GDAR) system is by far the most potent acid resistance system in commensal and pathogenic Listeria monocytogenes and requires the activity of intracellular glutamate decarboxylase GadB performing a proton-consuming decarboxylation reaction and the cognate antiporter GadC, which performs the glutamate/in/gamma-aminobutyrate/out electrogenic antiport, overview Listeria monocytogenes