The crystal structure of butyryl-CoA dehydrogenase (BCAD) from Megasphaera elsdenii complexed with acetoacetyl-CoA has been solved at 2.5 A resolution. The enzyme crystallizes in the P422 space group with cell dimensions a = b = 107.76 A and c = 153.67 A. BCAD is a bacterial analog of short chain acyl-CoA dehydrogenase from mammalian mitochondria. Mammalian acyl-CoA dehydrogenases are flavin adenine dinucleotide (FAD)-containing enzymes that catalyze the first step in the beta-oxidation of fatty acids. Although specific for substrate chain lengths, they exhibit high sequence homology. The structure of BCAD was solved by the molecular replacement method using the atomic coordinates of pig liver medium chain acyl-CoA dehydrogenase (MCAD). The structure was refined to an R-factor of 19.3%. The overall polypeptide fold of BCAD is similar to that of MCAD. E367 in BCAD is at the same position and in a similar conformation as the catalytic base in MCAD, E376. The main enzymatic differences between BCAD and MCAD are their substrate specificities and the significant oxygen reactivity exhibited by BCAD but not by MCAD. The substrate binding cavity of BCAD is relatively shallow compared to that of MCAD, as consequences of both a single amino acid insertion and differences in the side chains of the helices that make the binding site. The si-face of the FAD in BCAD is more exposed to solvent than that in MCAD. Therefore solvation can stabilize the superoxide anion and considerably increase the rate of oxidation of reduced flavin in the bacterial enzyme.
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