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PDBsum entry 2okj

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protein ligands Protein-protein interface(s) links
Lyase PDB id
2okj
Jmol
Contents
Protein chain
501 a.a. *
Ligands
ABU
ABU-PLZ
Waters ×359
* Residue conservation analysis
PDB id:
2okj
Name: Lyase
Title: The x-ray crystal structure of the 67kda isoform of glutamic acid decarboxylase (gad67)
Structure: Glutamate decarboxylase 1. Chain: a, b. Synonym: glutamate decarboxylase 67 kda isoform, gad-67, 67 kda glutamic acid decarboxylase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gad1, gad, gad67. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
2.30Å     R-factor:   0.188     R-free:   0.222
Authors: A.M.Buckle,G.Fenalti,R.H.P.Law,J.C.Whisstock
Key ref:
G.Fenalti et al. (2007). GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop. Nat Struct Biol, 14, 280-286. PubMed id: 17384644 DOI: 10.1038/nsmb1228
Date:
17-Jan-07     Release date:   27-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q99259  (DCE1_HUMAN) -  Glutamate decarboxylase 1
Seq:
Struc:
 
Seq:
Struc:
594 a.a.
501 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.15  - Glutamate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate = 4-aminobutanoate + CO2
L-glutamate
=
4-aminobutanoate
Bound ligand (Het Group name = ABU)
corresponds exactly
+ CO(2)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLZ) matches with 65.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carboxylic acid metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsmb1228 Nat Struct Biol 14:280-286 (2007)
PubMed id: 17384644  
 
 
GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop.
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, J.C.Whisstock.
 
  ABSTRACT  
 
Gamma-aminobutyric acid (GABA) is synthesized by two isoforms of the pyridoxal 5'-phosphate-dependent enzyme glutamic acid decarboxylase (GAD65 and GAD67). GAD67 is constitutively active and is responsible for basal GABA production. In contrast, GAD65, an autoantigen in type I diabetes, is transiently activated in response to the demand for extra GABA in neurotransmission, and cycles between an active holo form and an inactive apo form. We have determined the crystal structures of N-terminal truncations of both GAD isoforms. The structure of GAD67 shows a tethered loop covering the active site, providing a catalytic environment that sustains GABA production. In contrast, the same catalytic loop is inherently mobile in GAD65. Kinetic studies suggest that mobility in the catalytic loop promotes a side reaction that results in cofactor release and GAD65 autoinactivation. These data reveal the molecular basis for regulation of GABA homeostasis.
 
  Selected figure(s)  
 
Figure 2.
(a) The N-terminal (blue), PLP-binding (cyan) and C-terminal (green) domains are labeled. Monomer A is colored slightly lighter than monomer B. In the active sites, the Lys405-PLP Schiff base and the PLP-GABA moiety are shown as orange spheres and bound GABA product as yellow spheres. The catalytic loop forms a flap over the active site of an adjacent monomer in trans and is colored magenta in each monomer. (b,c) Active sites of GAD67, showing a close-up of Lys-PLP (shown as orange sticks), PLP-GABA (dark gray) and noncovalently bound GABA (yellow) moieties. The 2F[o] – F[c] omit electron density of GAD67 contoured at 1 is also shown (mesh). Hydrogen bonds are shown as dotted lines, water molecules as red spheres. The side chain of Tyr434 from the catalytic loop of other monomer is shown in magenta. Protonation sites C4' and C are labeled.
Figure 4.
(a) Active site of GAD65. 2F[o] – F[c] omit electron density contoured at 1 is also shown (atoms from Lys-PLP and GABA omitted from density calculation). Lys-PLP moiety is shown as orange sticks; noncovalently bound GABA molecules are colored yellow and cyan. (b) Superposition of active site residues of GAD67 (green, monomer A; cyan, monomer B) and GAD65 (light brown). Both Tyr434 side chain conformations from the catalytic loops of GAD67 are shown. Tyr434 from monomer B (in cyan) enters the active site of monomer A. In this conformation, the hydroxyl group of Tyr434 is 2.8 Å from the C atom. (c) Interactions between catalytic loop and adjacent monomer. Residues that are different in GAD65 are colored orange. The alternative conformation of Tyr434 (from monomer B) is shown as mauve bonds. Phe283 of GAD65 is shown as yellow bonds. Residues in GAD65 corresponding to GAD67 residues 432–442 are disordered. The PLP moiety in the active site is shown as orange spheres, hydrogen bonds as dotted lines and water molecules as red spheres. (d) Surface representation of active site of GAD65, in similar orientation to that in Figure 2d. Lys396-PLP (orange), GABA product (yellow/cyan sticks).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2007, 14, 280-286) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20503259 A.Hänninen, M.Soilu-Hänninen, C.S.Hampe, A.Deptula, K.Geubtner, J.Ilonen, M.Knip, and H.Reijonen (2010).
Characterization of CD4+ T cells specific for glutamic acid decarboxylase (GAD65) and proinsulin in a patient with stiff-person syndrome but without type 1 diabetes.
  Diabetes Metab Res Rev, 26, 271-279.  
20730101 C.Nogues, H.Leh, C.G.Langendorf, R.H.Law, A.M.Buckle, and M.Buckle (2010).
Characterisation of peptide microarrays for studying antibody-antigen binding using surface plasmon resonance imagery.
  PLoS One, 5, e12152.  
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
19842059 G.Richardson, H.Ding, T.Rocheleau, G.Mayhew, E.Reddy, Q.Han, B.M.Christensen, and J.Li (2010).
An examination of aspartate decarboxylase and glutamate decarboxylase activity in mosquitoes.
  Mol Biol Rep, 37, 3199-3205.  
20805323 J.Kanaani, J.Kolibachuk, H.Martinez, and S.Baekkeskov (2010).
Two distinct mechanisms target GAD67 to vesicular pathways and presynaptic clusters.
  J Cell Biol, 190, 911-925.  
20520773 M.Rizzi, R.Knoth, C.S.Hampe, P.Lorenz, M.L.Gougeon, B.Lemercier, N.Venhoff, F.Ferrera, U.Salzer, H.J.Thiesen, H.H.Peter, U.A.Walker, and H.Eibel (2010).
Long-lived plasma cells and memory B cells produce pathogenic anti-GAD65 autoantibodies in Stiff Person Syndrome.
  PLoS One, 5, e10838.  
20405034 M.S.Baptista, C.V.Melo, M.Armelão, D.Herrmann, D.O.Pimentel, G.Leal, M.V.Caldeira, B.A.Bahr, M.Bengtson, R.D.Almeida, and C.B.Duarte (2010).
Role of the proteasome in excitotoxicity-induced cleavage of glutamic acid decarboxylase in cultured hippocampal neurons.
  PLoS One, 5, e10139.  
19413567 A.A.Moya-García, A.Pino-Angeles, R.Gil-Redondo, A.Morreale, and F.Sánchez-Jiménez (2009).
Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition.
  Br J Pharmacol, 157, 4.  
19496167 A.Sergeeva, and H.T.Jansen (2009).
Neuroanatomical plasticity in the gonadotropin-releasing hormone system of the ewe: seasonal variation in glutamatergic and gamma-aminobutyric acidergic afferents.
  J Comp Neurol, 515, 615-628.  
18926919 N.Wegner, R.Wait, and P.J.Venables (2009).
Evolutionarily conserved antigens in autoimmune disease: implications for an infective aetiology.
  Int J Biochem Cell Biol, 41, 390-397.  
19300440 Y.G.Kim, S.Lee, O.S.Kwon, S.Y.Park, S.J.Lee, B.J.Park, and K.J.Kim (2009).
Redox-switch modulation of human SSADH by dynamic catalytic loop.
  EMBO J, 28, 959-968.
PDB codes: 2w8n 2w8o 2w8p 2w8q 2w8r
18514483 G.Fenalti, and M.J.Rowley (2008).
GAD65 as a prototypic autoantigen.
  J Autoimmun, 31, 228-232.  
18312293 H.Abdel-Halim, J.R.Hanrahan, D.E.Hibbs, G.A.Johnston, and M.Chebib (2008).
A molecular basis for agonist and antagonist actions at GABA(C) receptors.
  Chem Biol Drug Des, 71, 306-327.  
18040284 I.R.Mackay (2008).
Autoimmunity since the 1957 clonal selection theory: a little acorn to a large oak.
  Immunol Cell Biol, 86, 67-71.  
18270816 J.Wei, and J.Y.Wu (2008).
Post-translational regulation of L-glutamic acid decarboxylase in the brain.
  Neurochem Res, 33, 1459-1465.  
  18300057 R.Raju, and C.S.Hampe (2008).
Immunobiology of stiff-person syndrome.
  Int Rev Immunol, 27, 79-92.  
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.

 

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