Crystal structure of Escherichia coli GadB (neutral pH)

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 

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Crystal structure and functional analysis of escherichia coli glutamate decarboxylase

Capitani, G.De Biase, D.Aurizi, C.Gut, H.Bossa, F.Grutter, M.G.

(2003) EMBO J 22: 4027-4037

  • DOI: https://doi.org/10.1093/emboj/cdg403
  • Primary Citation of Related Structures:  
    1PMM, 1PMO

  • PubMed Abstract: 

    Glutamate decarboxylase is a vitamin B6-dependent enzyme, which catalyses the decarboxylation of glutamate to gamma-aminobutyrate. In Escherichia coli, expression of glutamate decarboxylase (GadB), a 330 kDa hexamer, is induced to maintain the physiological pH under acidic conditions, like those of the passage through the stomach en route to the intestine. GadB, together with the antiporter GadC, constitutes the gad acid resistance system, which confers the ability for bacterial survival for at least 2 h in a strongly acidic environment. GadB undergoes a pH-dependent conformational change and exhibits an activity optimum at low pH. We determined the crystal structures of GadB at acidic and neutral pH. They reveal the molecular details of the conformational change and the structural basis for the acidic pH optimum. We demonstrate that the enzyme is localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls. We show by structure-based site-directed mutagenesis that the triple helix bundle formed by the N-termini of the protein at acidic pH is the major determinant for this behaviour.

  • Organizational Affiliation

    Biochemisches Institut der Universität Zürich, Zürich CH-8057, Switzerland. capitani@bioc.unizh.ch

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
466Escherichia 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLR

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
N [auth C]
R [auth D]
AA [auth F],
G [auth A],
K [auth B],
N [auth C],
R [auth D],
V [auth E]
C8 H12 N O5 P
Query on TRS

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
DA [auth F]
H [auth A]
I [auth A]
BA [auth F],
CA [auth F],
DA [auth F],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth E]
C4 H12 N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.995α = 90
b = 115.995β = 90
c = 207.35γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations