Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


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

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

(2006) EMBO J 25: 2643-2651

  • DOI: https://doi.org/10.1038/sj.emboj.7601107
  • Primary Citation of Related Structures:  
    2DGK, 2DGL, 2DGM

  • PubMed 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.

  • Organizational Affiliation

    Biochemisches Institut der Universität Zürich, Zürich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate decarboxylase beta
A, B, C, D, E
A, B, C, D, E, F
452Escherichia coliMutation(s): 0 
Gene Names: gadB
Find proteins for P69910 (Escherichia coli (strain K12))
Explore P69910 
Go to UniProtKB:  P69910
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69910
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
O [auth C]
S [auth D]
V [auth E]
H [auth A],
K [auth B],
O [auth C],
S [auth D],
V [auth E],
Y [auth F]
C8 H10 N O6 P
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
N [auth C]
R [auth D]
U [auth E]
G [auth A],
J [auth B],
N [auth C],
R [auth D],
U [auth E],
X [auth F]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth B]
P [auth C]
Q [auth C]
I [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.77α = 90
b = 158.56β = 90
c = 201.42γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description