PDBsum entry 1d7r

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protein ligands metals links
Lyase PDB id
Protein chain
431 a.a. *
Waters ×130
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with 5pa
Structure: Protein (2,2-dialkylglycine decarboxylase (pyruvate)). Chain: a. Synonym: dgd. Engineered: yes
Source: Burkholderia cepacia. Organism_taxid: 292. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
2.00Å     R-factor:   0.215    
Authors: V.N.Malashkevich,M.D.Toney,P.Strop,J.Keller,J.N.Jansonius
Key ref:
V.N.Malashkevich et al. (1999). Crystal structures of dialkylglycine decarboxylase inhibitor complexes. J Mol Biol, 294, 193-200. PubMed id: 10556038 DOI: 10.1006/jmbi.1999.3254
19-Oct-99     Release date:   19-Nov-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P16932  (DGDA_BURCE) -  2,2-dialkylglycine decarboxylase
433 a.a.
431 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 2,2-dialkylglycine decarboxylase (pyruvate).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2,2-dialkylglycine + pyruvate = dialkyl ketone + CO2 + L-alanine
+ pyruvate
= dialkyl ketone
+ CO(2)
+ L-alanine
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = 5PA) 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     metabolic process   1 term 
  Biochemical function     catalytic activity     6 terms  


DOI no: 10.1006/jmbi.1999.3254 J Mol Biol 294:193-200 (1999)
PubMed id: 10556038  
Crystal structures of dialkylglycine decarboxylase inhibitor complexes.
V.N.Malashkevich, P.Strop, J.W.Keller, J.N.Jansonius, M.D.Toney.
The crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observed in previous structures that differ in alkali metal ion content, and two active-site conformations have been shown to coexist in solution when a single type of metal ion is present. There is no indication of coexisting conformers in the structures reported here or in the previously reported structures, and the observed conformation is that expected based on the presence of potassium in the enzyme. Thus, although two active-site conformations coexist in solution, a single conformation, corresponding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the aldimine double bond to the pyridoxal phosphate cofactor to be fully out of the plane of the coenzyme ring, whereas the Calpha-CO2(-) bond lies close to it. This provides an explanation for the observed lack of decarboxylation reactivity with this amino acid. The carboxylate groups of both 1-aminocyclopropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally that alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction. The structures of d and l-cycloserine bound to the active-site show that the l-isomer is deprotonated at C(alpha), presumably by Lys272, while the d-isomer is not. This difference explains the approximately 3000-fold greater potency of the l versus the d-isomer as a competitive inhibitor of dialkylglycine decarboxylase.
  Selected figure(s)  
Figure 1.
Figure 1. Chemical structures of the inhibitors employed in this study.
Figure 4.
Figure 4. Overlay of the active-site regions for the ACC (green) and PPL-MeAla (colored by atom type) structures. Note the non-planarity of the ACC aldimine with the coenzyme ring. This may be the cause of the lack of decarboxy- lation reactivity of this amino acid.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 294, 193-200) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445930 J.Lowther, B.A.Yard, K.A.Johnson, L.G.Carter, V.T.Bhat, M.C.Raman, D.J.Clarke, B.Ramakers, S.A.McMahon, J.H.Naismith, and D.J.Campopiano (2010).
Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation.
  Mol Biosyst, 6, 1682-1693.
PDB code: 2xbn
12429098 B.W.Noland, J.M.Newman, J.Hendle, J.Badger, J.A.Christopher, J.Tresser, M.D.Buchanan, T.A.Wright, M.E.Rutter, W.E.Sanderson, H.J.Müller-Dieckmann, K.S.Gajiwala, and S.G.Buchanan (2002).
Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme.
  Structure, 10, 1569-1580.
PDB codes: 1mdo 1mdx 1mdz
11939774 C.G.Cheong, C.B.Bauer, K.R.Brushaber, J.C.Escalante-Semerena, and I.Rayment (2002).
Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica.
  Biochemistry, 41, 4798-4808.
PDB codes: 1kus 1lkc
12119022 C.G.Cheong, J.C.Escalante-Semerena, and I.Rayment (2002).
Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
  Biochemistry, 41, 9079-9089.
PDB codes: 1l4b 1l4e 1l4f 1l4g 1l4h 1l4k 1l4l 1l4m 1l4n 1l5f 1l5k 1l5l 1l5m 1l5n 1l5o 1lc5 1lc7 1lc8
11170465 M.D.Toney (2001).
Computational studies on nonenzymatic and enzymatic pyridoxal phosphate catalyzed decarboxylations of 2-aminoisobutyrate.
  Biochemistry, 40, 1378-1384.  
11685243 P.Burkhard, P.Dominici, C.Borri-Voltattorni, J.N.Jansonius, and V.N.Malashkevich (2001).
Structural insight into Parkinson's disease treatment from drug-inhibited DOPA decarboxylase.
  Nat Struct Biol, 8, 963-967.
PDB codes: 1js3 1js6
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 code is shown on the right.