PDBsum entry 1pmm

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Lyase PDB id
Protein chains
(+ 0 more) 450 a.a. *
PLP ×6
ACY ×6
Waters ×1842
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of escherichia coli gadb (low ph)
Structure: Glutamate decarboxylase beta. Chain: a, b, c, d, e, f. Synonym: gad-beta. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: gadb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
2.00Å     R-factor:   0.182     R-free:   0.213
Authors: G.Capitani,D.De Biase,C.Aurizi,H.Gut,F.Bossa,M.G.Grutter
Key ref: G.Capitani et al. (2003). Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase. EMBO J, 22, 4027-4037. PubMed id: 12912902
11-Jun-03     Release date:   17-Feb-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P69910  (DCEB_ECOLI) -  Glutamate decarboxylase beta
466 a.a.
450 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
= 4-aminobutanoate
Bound ligand (Het Group name = ACY)
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   3 terms 
  Biological process     carboxylic acid metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  


EMBO J 22:4027-4037 (2003)
PubMed id: 12912902  
Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase.
G.Capitani, D.De Biase, C.Aurizi, H.Gut, F.Bossa, M.G.Grütter.
Glutamate decarboxylase is a vitamin B6-dependent enzyme, which catalyses the decarboxylation of glutamate to gamma-aminobutyrate. In Escherichia coli, expression of glutamate decarboxylase (GadB), a 330 kDa hexamer, is induced to maintain the physiological pH under acidic conditions, like those of the passage through the stomach en route to the intestine. GadB, together with the antiporter GadC, constitutes the gad acid resistance system, which confers the ability for bacterial survival for at least 2 h in a strongly acidic environment. GadB undergoes a pH-dependent conformational change and exhibits an activity optimum at low pH. We determined the crystal structures of GadB at acidic and neutral pH. They reveal the molecular details of the conformational change and the structural basis for the acidic pH optimum. We demonstrate that the enzyme is localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls. We show by structure-based site-directed mutagenesis that the triple helix bundle formed by the N-termini of the protein at acidic pH is the major determinant for this behaviour.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20505866 A.Pessione, C.Lamberti, and E.Pessione (2010).
Proteomics as a tool for studying energy metabolism in lactic acid bacteria.
  Mol Biosyst, 6, 1419-1430.  
20453931 B.Zhao, and W.A.Houry (2010).
Acid stress response in enteropathogenic gammaproteobacteria: an aptitude for survival.
  Biochem Cell Biol, 88, 301-314.  
19915035 C.H.Martin, D.Wu, and K.L.Prather (2010).
Integrated bioprocessing for the pH-dependent production of 4-valerolactone from levulinate in Pseudomonas putida KT2440.
  Appl Environ Microbiol, 76, 417-424.  
20696404 F.Bourquin, H.Riezman, G.Capitani, and M.G.Grütter (2010).
Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism.
  Structure, 18, 1054-1065.
PDB codes: 3mad 3maf 3mau 3mbb 3mc6
20364279 H.Li, and Y.Cao (2010).
Lactic acid bacterial cell factories for gamma-aminobutyric acid.
  Amino Acids, 39, 1107-1116.  
20374524 L.Avesani, A.Vitale, E.Pedrazzini, M.Devirgilio, A.Pompa, A.Barbante, E.Gecchele, P.Dominici, F.Morandini, A.Brozzetti, A.Falorni, and M.Pezzotti (2010).
Recombinant human GAD65 accumulates to high levels in transgenic tobacco plants when expressed as an enzymatically inactive mutant.
  Plant Biotechnol J, 8, 862-872.  
20673017 L.Avesani, L.Bortesi, L.Santi, A.Falorni, and M.Pezzotti (2010).
Plant-made pharmaceuticals for the prevention and treatment of autoimmune diseases: where are we?
  Expert Rev Vaccines, 9, 957-969.  
19797049 E.Pennacchietti, T.M.Lammens, G.Capitani, M.C.Franssen, R.A.John, F.Bossa, and D.De Biase (2009).
Mutation of His465 alters the pH-dependent spectroscopic properties of Escherichia coli glutamate decarboxylase and broadens the range of its activity toward more alkaline pH.
  J Biol Chem, 284, 31587-31596.  
19129626 H.W.Kim, Y.Kashima, K.Ishikawa, and N.Yamano (2009).
Purification and characterization of the first archaeal glutamate decarboxylase from Pyrococcus horikoshii.
  Biosci Biotechnol Biochem, 73, 224-227.  
19813213 R.Pieper, Q.Zhang, P.P.Parmar, S.T.Huang, D.J.Clark, H.Alami, A.Donohue-Rolfe, R.D.Fleischmann, S.N.Peterson, and S.Tzipori (2009).
The Shigella dysenteriae serotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins.
  Proteomics, 9, 5029-5045.  
18487605 D.Mukhopadhyay, K.S.Howell, H.Riezman, and G.Capitani (2008).
Identifying key residues of sphinganine-1-phosphate lyase for function in vivo and in vitro.
  J Biol Chem, 283, 20159-20169.  
18256502 N.Komatsuzaki, T.Nakamura, T.Kimura, and J.Shima (2008).
Characterization of glutamate decarboxylase from a high gamma-aminobutyric acid (GABA)-producer, Lactobacillus paracasei.
  Biosci Biotechnol Biochem, 72, 278-285.  
17937401 O.Almog, A.Kogan, M.Leeuw, G.Y.Gdalevsky, R.Cohen-Luria, and A.H.Parola (2008).
Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41.
  Biopolymers, 89, 354-359.  
17384644 G.Fenalti, R.H.Law, A.M.Buckle, C.Langendorf, K.Tuck, C.J.Rosado, N.G.Faux, K.Mahmood, C.S.Hampe, J.P.Banga, M.Wilce, J.Schmidberger, J.Rossjohn, O.El-Kabbani, R.N.Pike, A.I.Smith, I.R.Mackay, M.J.Rowley, and J.C.Whisstock (2007).
GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop.
  Nat Struct Mol Biol, 14, 280-286.
PDB codes: 2okj 2okk
16980449 A.Tramonti, M.De Canio, I.Delany, V.Scarlato, and D.De Biase (2006).
Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli.
  J Bacteriol, 188, 8118-8127.  
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
15735332 D.I.Dutyshev, E.L.Darii, N.P.Fomenkova, I.V.Pechik, K.M.Polyakov, S.V.Nikonov, N.S.Andreeva, and B.S.Sukhareva (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.
PDB code: 1xey
15690345 G.Capitani, D.De Biase, H.Gut, S.Ahmed, and M.G.Grütter (2005).
Structural model of human GAD65: prediction and interpretation of biochemical and immunogenic features.
  Proteins, 59, 7.  
15791207 T.Nakai, N.Nakagawa, N.Maoka, R.Masui, S.Kuramitsu, and N.Kamiya (2005).
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.
  EMBO J, 24, 1523-1536.
PDB codes: 1wyt 1wyu 1wyv
15494746 J.W.Foster (2004).
Escherichia coli acid resistance: tales of an amateur acidophile.
  Nat Rev Microbiol, 2, 898-907.  
14731280 M.Metzner, J.Germer, and R.Hengge (2004).
Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli.
  Mol Microbiol, 51, 799-811.  
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.