1XEY

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

Summary for 1XEY

• Entry DOI: 10.2210/pdb1xey/pdb
• Descriptor: Glutamate decarboxylase alpha, ACETATE ION, PYRIDOXAL-5'-PHOSPHATE, ... (5 entities in total)
• Functional Keywords: lyase, glutamate decarboxylase, complex with glutarate
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 106364.56

Authors

Dutyshev, D.I.,Darii, E.L.,Fomenkova, N.P.,Pechik, I.V.,Polyakov, K.M.,Nikonov, S.V.,Andreeva, N.S.,Sukhareva, B.S. (deposition date: 2004-09-13, release date: 2004-10-05, Last modification date: 2023-08-23)

Primary citation

Dutyshev, D.I.,Darii, E.L.,Fomenkova, N.P.,Pechik, I.V.,Polyakov, K.M.,Nikonov, S.V.,Andreeva, N.S.,Sukhareva, B.S.
Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution.
Acta Crystallogr.,Sect.D, 61:230-235, 2005

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.

PubMed: 15735332
DOI: 10.1107/S0907444904032147

Experimental method

X-RAY DIFFRACTION (2.05 Å)