PDBsum entry 1xey

Lyase

PDB id: 1xey

Contents

Protein chains

448 a.a. *

Ligands

ACT ×2

PLP ×2

GUA ×2

Waters ×390

* Residue conservation analysis

PDB id:

1xey

Name:

Lyase

Title:

Crystal structure of the complex of escherichia coli gada with glutarate at 2.05 a resolution

Structure:

Glutamate decarboxylase alpha. Chain: a, b. Synonym: gad-alpha. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: gada. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.05Å R-factor: 0.151 R-free: 0.199

Authors:

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

Key ref:

D.I.Dutyshev et al. (2005). Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution. Acta Crystallogr D Biol Crystallogr, 61, 230-235. PubMed id: 15735332 DOI: 10.1107/S0907444904032147

Date:

13-Sep-04 Release date: 05-Oct-04

Protein chains

P69908  (DCEA_ECOLI) -  Glutamate decarboxylase alpha from Escherichia coli (strain K12)

Seq: 466 a.a.

Struc: 448 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.15 - glutamate decarboxylase.
• Reaction: L-glutamate + H⁺ = 4-aminobutanoate + CO2

L-glutamate + H(+) (Bound ligand (Het Group name = GUA) matches with 90.00% similarity) = 4-aminobutanoate + CO2 (Bound ligand (Het Group name = ACT) matches with 75.00% similarity)

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444904032147

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

PubMed id: 15735332

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

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

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.

Selected figure(s)

Figure 1.
Figure 1 Stereographic projection along the z axis of the self-rotation function for the twofold axis (peak heights corresponding to the noncrystallographic twofold axis are 76% of the height of the peak corresponding to the crystallographic threefold axis).

Figure 4.
Figure 4 Scheme of the active site in GAD [170][alpha] . The C, O and N atoms are black, red and blue, respectively. The glutarate and PLP molecules are coloured violet. Hydrogen bonds are indicated by green dashed lines. The figure was generated using the LIGPLOT program (Wallace et al., 1995[171] [Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). Protein Eng. 8, 127-134.]-[172][bluearr.gif] ).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 230-235) copyright 2005.

Figures were selected by an automated process.