2dgl

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2dgl, resolution 3.15Å ()
Ligands: , ,
Gene: gadB (Escherichia coli)
Activity: Glutamate decarboxylase, with EC number 4.1.1.15
Related: 1pmm, 1pmo, 2dgk, 2dgm
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Crystal structure of Escherichia coli GadB in complex with bromide

Publication Abstract from PubMed

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.

Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB., Gut H, Pennacchietti E, John RA, Bossa F, Capitani G, De Biase D, Grutter MG, EMBO J. 2006 Jun 7;25(11):2643-51. Epub 2006 May 4. PMID:16675957

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2dgl is a 6 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

  • Gut H, Pennacchietti E, John RA, Bossa F, Capitani G, De Biase D, Grutter MG. Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. EMBO J. 2006 Jun 7;25(11):2643-51. Epub 2006 May 4. PMID:16675957
  • Capitani G, De Biase D, Aurizi C, Gut H, Bossa F, Grutter MG. Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase. EMBO J. 2003 Aug 15;22(16):4027-37. PMID:12912902 doi:http://dx.doi.org/10.1093/emboj/cdg403

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