1VFT image
Deposition Date 2004-04-19
Release Date 2004-09-14
Last Version Date 2023-11-15
Entry Detail
PDB ID:
1VFT
Keywords:
Title:
Crystal structure of L-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.28
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:alanine racemase
Gene (Uniprot):alr
Chain IDs:A, B
Chain Length:386
Number of Molecules:2
Biological Source:Streptomyces lavendulae
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX A LYS LYSINE NZ-CARBOXYLIC ACID
Primary Citation
Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.
J.Biol.Chem. 279 46153 46161 (2004)
PMID: 15302886 DOI: 10.1074/jbc.M404605200

Abstact

Alanine racemase (ALR), an enzyme that catalyzes the interconversion of Ala enantiomers, is essential for the synthesis of the bacterial cell wall. We have shown that it is harder to inhibit the catalytic activity of ALR from D-cycloserine (DCS)-producing Streptomyces lavendulae than that from Escherichia coli by DCS. To obtain structural evidence for the fact that Streptomyces ALR displays resistance to DCS, we determined the precise nature of the x-ray crystal structures of the cycloserine-free and cycloserine enantiomer-bound forms of Streptomyces ALR at high resolutions. Streptomyces ALR takes a dimer structure, which is formed by interactions between the N-terminal domain of one monomer with the C-terminal domain of its partner. Each of the two active sites of ALR, which is generated as a result of the formation of the dimer structure, is composed of pyridoxal 5'-phosphate (PLP), the PLP-binding residue Lys(38), and the amino acids in the immediate environment of the pyridoxal cofactor. The current model suggests that each active site of Streptomyces ALR maintains a larger space and takes a more rigid conformation than that of Bacillus stearothermophilus ALR determined previously. Furthermore, we show that Streptomyces ALR results in a slow conversion to a final form of a pyridoxal derivative arising from either isomer of cycloserine, which inhibits the catalytic activity noncompetitively. In fact, the slow conversion is confirmed by the fact that each enzyme bound cycloserine derivative, which is bound to PLP, takes an asymmetric structure.

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