The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid

The X-ray structure of the complex formed between yeast 5-aminolaevulinic a cid dehydratase (ALAD) and the inhibitor laevulinic acid has been determine d at 2.15 Angstrom resolution. The inhibitor binds by forming a Schiff base link with one of the two invariant lysines at the catalytic center: Lys263 . It is known that this lysine forms a Schiff base link with substrate boun d at the enzyme's so-called P-site. The carboxyl group of laevulinic acid m akes hydrogen bonds with the side-chain-OH groups of Tyr329 and Ser290, as well as with the main-chain >NH group of Ser290. The aliphatic moiety of th e inhibitor makes hydrophobic interactions with surrounding aromatic residu es in the protein including Phe219, which resides in the flap covering the active site. Our analysis strongly suggests that the same interactions will be made by P-side substrate and also indicates that the substrate that bin ds at the enzyme's A-site will interact with the enzyme's zinc ion bound by three cysteines (133, 135, and 143). Inhibitor binding caused a substantia l ordering of the active site nap (residues 217-235, which was largely invi sible in the native electron density map and indicates that this highly con served yet flexible region has a specific role in substrate binding during catalysis.