Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 318.21 kDa 
• Atom Count: 23447 
• Modelled Residue Count: 2698 
• Deposited Residue Count: 2796 
• Unique protein chains: 1

1PMM

Crystal structure of Escherichia coli GadB (low pH)

• PDB DOI: 10.2210/pdb1PMM/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-11 Released: 2004-02-17 
• Deposition Author(s): Capitani, G., De Biase, D., Aurizi, C., Gut, H., Bossa, F., Grutter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 

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

• PubMed: 12912902 
• DOI: 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.

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Organizational Affiliation: 

Biochemisches Institut der Universität Zürich, Zürich CH-8057, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase beta	A, B, C, D, E, F	466	Escherichia coli	Mutation(s): 0  Gene Names: gadB EC: 4.1.1.15
UniProt
Find proteins for P69910 (Escherichia coli (strain K12)) Explore P69910  Go to UniProtKB:  P69910

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], R [auth F]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ACY	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], Q [auth E]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.78	α = 76.8
b = 91.406	β = 77.1
c = 93.686	γ = 78.24

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-11 
• Released Date: 2004-02-17 
Deposition Author(s): Capitani, G., De Biase, D., Aurizi, C., Gut, H., Bossa, F., Grutter, M.G.

Revision History  

• 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: Non-polymer description, Version format compliance