PDBsum entry: 2dgl

Lyase

PDB id: 2dgl

Contents

Protein chains

(+ 0 more) 450 a.a. *

Ligands

PLP ×6

ACY ×6

Metals

_BR ×24

Waters ×134

* Residue conservation analysis

PDB id:

2dgl

Name:

Lyase

Title:

Crystal structure of escherichia coli gadb in complex with b

Structure:

Glutamate decarboxylase beta. Chain: a, b, c, d, e, f. Synonym: gad-beta, gadb. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: jm109. Gene: gadb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

3.15Å R-factor: 0.218 R-free: 0.248

Authors:

M.G.Gruetter,G.Capitani,H.Gut

Key ref:

H.Gut et al. (2006). Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. EMBO J, 25, 2643-2651. PubMed id: 16675957 DOI: 10.1038/sj.emboj.7601107

Date:

14-Mar-06 Release date: 20-Jun-06

Protein chains

P69910  (DCEB_ECOLI) -  Glutamate decarboxylase beta

Seq: 466 a.a.

Struc: 450 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.15 - Glutamate decarboxylase.
• Reaction: L-glutamate = 4-aminobutanoate + CO₂

L-glutamate = 4-aminobutanoate + CO(2) (Bound ligand (Het Group name = ACY) matches with 75.00% similarity)

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (3 terms)
• Biological process: carboxylic acid metabolic process (3 terms)
• Biochemical function: catalytic activity (8 terms)

reference

DOI no: 10.1038/sj.emboj.7601107

EMBO J 25:2643-2651 (2006)

PubMed id: 16675957

Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB.

H.Gut, E.Pennacchietti, R.A.John, F.Bossa, G.Capitani, D.De Biase, M.G.Grütter.

ABSTRACT

Escherichia coli and other enterobacteria exploit the H+ -consuming reaction catalysed by glutamate decarboxylase to survive the stomach acidity before reaching the intestine. Here we show that chloride, extremely abundant in gastric secretions, is an allosteric activator producing a 10-fold increase in the decarboxylase activity at pH 5.6. Cooperativity and sensitivity to chloride were lost when the N-terminal 14 residues, involved in the formation of two triple-helix bundles, were deleted by mutagenesis. X-ray structures, obtained in the presence of the substrate analogue acetate, identified halide-binding sites at the base of each N-terminal helix, showed how halide binding is responsible for bundle stability and demonstrated that the interconversion between active and inactive forms of the enzyme is a stepwise process. We also discovered an entirely novel structure of the cofactor pyridoxal 5'-phosphate (aldamine) to be responsible for the reversibly inactivated enzyme. Our results link the entry of chloride ions, via the H+/Cl- exchange activities of ClC-ec1, to the trigger of the acid stress response in the cell when the intracellular proton concentration has not yet reached fatal values.

Selected figure(s)

Figure 2.
Figure 2 Halide binding to the N-terminal region of GadB. (A) Side view of GadB in its active (low pH) conformation (1PMM) with the helix bundles protruding from top and bottom of the hexamer. (B) Detailed view of the iodide-binding site S1 with one helix bundle partly visible. Residues interacting with the ion are depicted in blue and orange. Chloride anomalous difference density contoured at 2.8 is superimposed on the GadB–I^- structure. (C) View along the three-fold axis of GadB onto the N-terminal three helical bundle (in red) with bound bromide ions (S1, S2, S3). Bromide ions appear as brown spheres with Bijvoet difference-Fourier electron density in green contoured at 3.3 .

Figure 4.
Figure 4 Stereo view of the substituted aldamine in the active site of GadB 1–14. The C-terminal residues 463–466, the PLP-cofactor and Lys276 appear as sticks (orange and atom colours, while other residues are in white and atom colours) with the corresponding 2mF[o]-DF[c] electron density (1 ). Both the epsilon -nitrogen of Lys276 and the distal side chain nitrogen of His465 form a covalent bond with the C4' atom (hybridized sp^3) of the PLP-cofactor.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 2643-2651) copyright 2006.

Figures were selected by an automated process.