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.
