1PMO

Crystal structure of Escherichia coli GadB (neutral pH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1093/emboj/cdg403
  • Primary Citation of Related Structures:  1PMM
  • Also Cited By: 2DGK, 2DGL, 2DGM

  • 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 physio ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate decarboxylase beta
A, B, C, D, E, F
466Escherichia coli (strain K12)Gene Names: gadB
EC: 4.1.1.15
Find proteins for P69910 (Escherichia coli (strain K12))
Go to UniProtKB:  P69910
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D, E, F
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PLR
Query on PLR

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
4'-DEOXYPYRIDOXINE PHOSPHATE
C8 H12 N O5 P
RBCOYOYDYNXAFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 115.995α = 90.00
b = 115.995β = 90.00
c = 207.350γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance