PDBsum entry 2dgk

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Lyase PDB id
Protein chains
(+ 0 more) 438 a.a. *
SO4 ×6
PLP ×6
EDO ×8
Waters ×1695
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of an n-terminal deletion mutant of escher gadb in an autoinhibited state (aldamine)
Structure: Glutamate decarboxylase beta. Chain: a, b, c, d, e, f. Fragment: gadbd1-14. Synonym: gad-beta, gadb. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: jm109. Gene: gadb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
1.90Å     R-factor:   0.218     R-free:   0.246
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
14-Mar-06     Release date:   20-Jun-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P69910  (DCEB_ECOLI) -  Glutamate decarboxylase beta
466 a.a.
438 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glutamate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate = 4-aminobutanoate + CO2
= 4-aminobutanoate
Bound ligand (Het Group name = EDO)
matches with 40.00% 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 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     carboxylic acid metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21464825 T.A.Krulwich, G.Sachs, and E.Padan (2011).
Molecular aspects of bacterial pH sensing and homeostasis.
  Nat Rev Microbiol, 9, 330-343.  
20505866 A.Pessione, C.Lamberti, and E.Pessione (2010).
Proteomics as a tool for studying energy metabolism in lactic acid bacteria.
  Mol Biosyst, 6, 1419-1430.  
20453931 B.Zhao, and W.A.Houry (2010).
Acid stress response in enteropathogenic gammaproteobacteria: an aptitude for survival.
  Biochem Cell Biol, 88, 301-314.  
21034467 E.Krin, A.Danchin, and O.Soutourina (2010).
Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli.
  BMC Microbiol, 10, 273.  
20696404 F.Bourquin, H.Riezman, G.Capitani, and M.G.Grütter (2010).
Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism.
  Structure, 18, 1054-1065.
PDB codes: 3mad 3maf 3mau 3mbb 3mc6
20374524 L.Avesani, A.Vitale, E.Pedrazzini, M.Devirgilio, A.Pompa, A.Barbante, E.Gecchele, P.Dominici, F.Morandini, A.Brozzetti, A.Falorni, and M.Pezzotti (2010).
Recombinant human GAD65 accumulates to high levels in transgenic tobacco plants when expressed as an enzymatically inactive mutant.
  Plant Biotechnol J, 8, 862-872.  
20013120 R.Di Cagno, F.Mazzacane, C.G.Rizzello, M.De Angelis, G.Giuliani, M.Meloni, B.De Servi, and M.Gobbetti (2010).
Synthesis of gamma-aminobutyric acid (GABA) by Lactobacillus plantarum DSM19463: functional grape must beverage and dermatological applications.
  Appl Microbiol Biotechnol, 86, 731-741.  
19898476 A.Picollo, M.Malvezzi, J.C.Houtman, and A.Accardi (2009).
Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters.
  Nat Struct Mol Biol, 16, 1294-1301.  
  19241380 A.S.Olia, S.Casjens, and G.Cingolani (2009).
Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.
  Protein Sci, 18, 537-548.
PDB code: 3c9i
19797049 E.Pennacchietti, T.M.Lammens, G.Capitani, M.C.Franssen, R.A.John, F.Bossa, and D.De Biase (2009).
Mutation of His465 alters the pH-dependent spectroscopic properties of Escherichia coli glutamate decarboxylase and broadens the range of its activity toward more alkaline pH.
  J Biol Chem, 284, 31587-31596.  
19542291 L.Slamti, and M.K.Waldor (2009).
Genetic analysis of activation of the Vibrio cholerae Cpx pathway.
  J Bacteriol, 191, 5044-5056.  
18487605 D.Mukhopadhyay, K.S.Howell, H.Riezman, and G.Capitani (2008).
Identifying key residues of sphinganine-1-phosphate lyase for function in vivo and in vitro.
  J Biol Chem, 283, 20159-20169.  
18460820 K.Hiraga, Y.Ueno, and K.Oda (2008).
Glutamate decarboxylase from Lactobacillus brevis: activation by ammonium sulfate.
  Biosci Biotechnol Biochem, 72, 1299-1306.  
18256502 N.Komatsuzaki, T.Nakamura, T.Kimura, and J.Shima (2008).
Characterization of glutamate decarboxylase from a high gamma-aminobutyric acid (GABA)-producer, Lactobacillus paracasei.
  Biosci Biotechnol Biochem, 72, 278-285.  
17598751 B.S.Hughes, A.J.Cullum, and A.F.Bennett (2007).
Evolutionary adaptation to environmental pH in experimental lineages of Escherichia coli.
  Evolution Int J Org Evolution, 61, 1725-1734.  
17384644 G.Fenalti, R.H.Law, A.M.Buckle, C.Langendorf, K.Tuck, C.J.Rosado, N.G.Faux, K.Mahmood, C.S.Hampe, J.P.Banga, M.Wilce, J.Schmidberger, J.Rossjohn, O.El-Kabbani, R.N.Pike, A.I.Smith, I.R.Mackay, M.J.Rowley, and J.C.Whisstock (2007).
GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop.
  Nat Struct Mol Biol, 14, 280-286.
PDB codes: 2okj 2okk
16980449 A.Tramonti, M.De Canio, I.Delany, V.Scarlato, and D.De Biase (2006).
Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli.
  J Bacteriol, 188, 8118-8127.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.