PDBsum entry 1xey

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Lyase PDB id
Jmol PyMol
Protein chains
448 a.a. *
ACT ×2
PLP ×2
GUA ×2
Waters ×390
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the complex of escherichia coli gada wi 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)
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
13-Sep-04     Release date:   05-Oct-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P69908  (DCEA_ECOLI) -  Glutamate decarboxylase alpha
466 a.a.
448 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glutamate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate = 4-aminobutanoate + CO2
Bound ligand (Het Group name = GUA)
matches with 90.00% similarity
= 4-aminobutanoate
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     carboxylic acid metabolic process   3 terms 
  Biochemical function     protein binding     5 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20453931 B.Zhao, and W.A.Houry (2010).
Acid stress response in enteropathogenic gammaproteobacteria: an aptitude for survival.
  Biochem Cell Biol, 88, 301-314.  
18460820 K.Hiraga, Y.Ueno, and K.Oda (2008).
Glutamate decarboxylase from Lactobacillus brevis: activation by ammonium sulfate.
  Biosci Biotechnol Biochem, 72, 1299-1306.  
16675957 H.Gut, E.Pennacchietti, R.A.John, F.Bossa, G.Capitani, D.De Biase, and M.G.Grütter (2006).
Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB.
  EMBO J, 25, 2643-2651.
PDB codes: 2dgk 2dgl 2dgm
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.