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,PQS (software)

Macromolecule Content

• Total Structure Weight: 106.36 kDa 
• Atom Count: 7612 
• Modelled Residue Count: 897 
• Deposited Residue Count: 932 
• Unique protein chains: 1

1XEY

Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution

• PDB DOI: 10.2210/pdb1XEY/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-09-13 Released: 2004-10-05 
• Deposition Author(s): Dutyshev, D.I., Darii, E.L., Fomenkova, N.P., Pechik, I.V., Polyakov, K.M., Nikonov, S.V., Andreeva, N.S., Sukhareva, B.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.199 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 

Literature

Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution.

Dutyshev, D.I., Darii, E.L., Fomenkova, N.P., Pechik, I.V., Polyakov, K.M., Nikonov, S.V., Andreeva, N.S., Sukhareva, B.S.

(2005) Acta Crystallogr D Biol Crystallogr 61: 230-235

• PubMed: 15735332 
• DOI: 10.1107/S0907444904032147
• Primary Citation of Related Structures:  
  1XEY


• PubMed Abstract: 
  

Glutamate decarboxylase (GAD) is a pyridoxal enzyme that catalyzes the conversion of L-glutamate into gamma-aminobutyric acid and carbon dioxide. The Escherichia coli enzyme exists as two isozymes, referred to as GADalpha and GADbeta. Crystals of the complex of the recombinant isozyme GADalpha with glutarate as a substrate analogue were grown in space group R3, with unit-cell parameters a = b = 117.1, c = 196.4 angstroms. The structure of the enzyme was solved by the molecular-replacement method and refined at 2.05 angstroms resolution to an R factor of 15.1% (R(free) = 19.9%). The asymmetric unit contains a dimer consisting of two subunits of the enzyme related by a noncrystallographic twofold axis which is perpendicular to and intersects a crystallographic threefold axis. The dimers are related by a crystallographic threefold axis to form a hexamer. The active site of each subunit is formed by residues of the large domains of both subunits of the dimer. The coenzyme pyridoxal phosphate (PLP) forms an aldimine bond with Lys276. The glutarate molecule bound in the active site of the enzyme adopts two conformations with equal occupancies. One of the two carboxy groups of the glutarate occupies the same position in both conformations and forms hydrogen bonds with the N atom of the main chain of Phe63 and the side chain of Thr62 of one subunit and the side chains of Asp86 and Asn83 of the adjacent subunit of the dimer. Apparently, it is in this position that the distal carboxy group of the substrate would be bound by the enzyme, thus providing recognition of glutamic acid by the enzyme.

---

Organizational Affiliation: 

V. A. Engelhardt Institute of Molecular Biology, RAS, 32 Vavilov Str., 119991 Moscow, Russia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase alpha	A, B	466	Escherichia coli	Mutation(s): 0  Gene Names: gadA EC: 4.1.1.15
UniProt
Find proteins for P69908 (Escherichia coli (strain K12)) Explore P69908  Go to UniProtKB:  P69908

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GUA	F [auth A], H [auth B]	GLUTARIC ACID C5 H8 O4 JFCQEDHGNNZCLN-UHFFFAOYSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.199 
• R-Value Work: 0.148 
• R-Value Observed: 0.151 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.1	α = 90
b = 117.1	β = 90
c = 196.4	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-13 
• Released Date: 2004-10-05 
Deposition Author(s): Dutyshev, D.I., Darii, E.L., Fomenkova, N.P., Pechik, I.V., Polyakov, K.M., Nikonov, S.V., Andreeva, N.S., Sukhareva, B.S.

Revision History  

• Version 1.0: 2004-10-05
  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