FMN-dependent alpha-hydroxy acid dehydrogenase signature and profile

A number of oxidoreductases that act on α-hydroxy acids and which are FMN-containing flavoproteins have been shown [1,2,3,4] to be structurally related; these enzymes are:

• Lactate dehydrogenase (EC 1.1.2.3), which consists of a dehydrogenase domain and a heme-binding domain called cytochrome b2 and which catalyzes the conversion of lactate into pyruvate.
• Glycolate oxidase (EC 1.1.3.15) ((S)-2-hydroxy-acid oxidase), a peroxisomal enzyme that catalyzes the conversion of glycolate and oxygen to glyoxylate and hydrogen peroxide.
• Long chain α-hydroxy acid oxidase from rat (EC 1.1.3.15), a peroxisomal enzyme.
• Lactate 2-monooxygenase (EC 1.13.12.4) (lactate oxidase) from Mycobacterium smegmatis, which catalyzes the conversion of lactate and oxygen to acetate, carbon dioxide and water.
• (S)-mandelate dehydrogenase from Pseudomonas putida (gene mdlB), which catalyzes the reduction of (S)-mandelate to benzoylformate.

The first step in the reaction mechanism of these enzymes is the abstraction of the proton from the α-carbon of the substrate producing a carbanion which can subsequently attach to the N5 atom of FMN. A conserved histidine has been shown [5] to be involved in the removal of the proton. We selected for a signature pattern the region around this active site residue, which is highly conserved and contains an arginine residue which is involved in substrate binding. Three-dimensional structures of FMN-dependent α-hydroxy acid dehydrogenases show a common fold with a TIM barrel structure (see <PDB:1TB3>). We also developed a profile that covers the entire FMN hydroxy acid dehydrogenase domain.