PDBsum entry: 1d7r

Lyase

PDB id: 1d7r

Contents

Protein chain

431 a.a. *

Ligands

5PA

Metals

_NA

__K

Waters ×130

* Residue conservation analysis

PDB id:

1d7r

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)

Resolution:

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

Date:

19-Oct-99 Release date: 19-Nov-99

Protein chain

P16932  (DGDA_BURCE) -  2,2-dialkylglycine decarboxylase

Seq: 433 a.a.

Struc: 431 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.64 - 2,2-dialkylglycine decarboxylase (pyruvate).
• Reaction: 2,2-dialkylglycine + pyruvate = dialkyl ketone + CO₂ + 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 

• Biochemical function: catalytic activity (6 terms)

reference

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.

ABSTRACT

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.