Biological Assembly 1  

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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: 106364.55 
• Atom Count: 7222 
• Residue Count: 932 
• Unique protein chains: 1

1XEY

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

• DOI: 10.2210/pdb1XEY/pdb

• Classification: LYASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21


• 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.

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Experimental Data Snapshot

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

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.,Sect.D 61: 230-235

• PubMed: 15735332 
• DOI: 10.1107/S0907444904032147


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GUA	A, B	GLUTARIC ACID C5 H8 O4 JFCQEDHGNNZCLN-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 117.100	α = 90.00
b = 117.100	β = 90.00
c = 196.400	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance