2SFP

ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR

Summary for 2SFP

• Entry DOI: 10.2210/pdb2sfp/pdb
• Descriptor: PROTEIN (ALANINE RACEMASE), PYRIDOXAL-5'-PHOSPHATE, PROPANOIC ACID, ... (4 entities in total)
• Functional Keywords: racemase, isomerase, alanine, pyridoxal phosphate
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 2
• Total formula weight: 88032.58

Authors

Morollo, A.A.,Petsko, G.A.,Ringe, D. (deposition date: 1999-02-16, release date: 1999-02-24, Last modification date: 2023-11-15)

Primary citation

Morollo, A.A.,Petsko, G.A.,Ringe, D.
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
Biochemistry, 38:3293-3301, 1999

PubMed Abstract: The structure of alanine racemase from Bacillus stearothermophilus with the inhibitor propionate bound in the active site was determined by X-ray crystallography to a resolution of 1.9 A. The enzyme is a homodimer in solution and crystallizes with a dimer in the asymmetric unit. Both active sites contain a pyridoxal 5'-phosphate (PLP) molecule in aldimine linkage to Lys39 as a protonated Schiff base, and the pH-independence of UV-visible absorption spectra suggests that the protonated PLP-Lys39 Schiff base is the reactive form of the enzyme. The carboxylate group of propionate bound in the active site makes numerous interactions with active-site residues, defining the substrate binding site of the enzyme. The propionate-bound structure therefore approximates features of the Michaelis complex formed between alanine racemase and its amino acid substrate. The structure also provides evidence for the existence of a carbamate formed on the side-chain amino group of Lys129, stabilized by interactions with one of the residues interacting with the carboxylate group of propionate, Arg136. We propose that this novel interaction influences both substrate binding and catalysis by precisely positioning Arg136 and modulating its charge.

PubMed: 10079072
DOI: 10.1021/bi9822729

Experimental method

X-RAY DIFFRACTION (1.9 Å)