Three-Dimensional Structure of the Flavoenzyme Acyl-CoA Oxidase-II from Rat Liver, the Peroxisomal Counterpart of Mitochondrial Acyl-CoA Dehydrogenase

Abstract

Acyl-CoA oxidase (ACO) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids. The crystal structure of ACO-II, which is one of two forms of rat liver ACO (ACO-I and ACO-II), has been solved and refined to an R-factor of 20.6% at 2.2-A resolution. The enzyme is a homodimer, and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain. The X-ray analysis showed that the overall folding of ACO-II less C-terminal 221 residues is similar to that of medium-chain acyl-CoA dehydrogenase (MCAD). However, the N-terminal alpha- and beta-domains rotate by 13 with respect to the C-terminal alpha-domain compared with those in MCAD to give a long and large crevice that accommodates the cofactor FAD and the substrate acyl-CoA. FAD is bound to the crevice between the beta- and C-terminal domains with its adenosine diphosphate portion interacting extensively with the other subunit of the molecule. The flavin ring of FAD resides at the active site with its si-face attached to the beta-domain, and is surrounded by active-site residues in a mode similar to that found in MCAD. However, the residues have weak interactions with the flavin ring due to the loss of some of the important hydrogen bonds with the flavin ring found in MCAD. The catalytic residue Glu421 in the C-terminal alpha-domain seems to be too far away from the flavin ring to abstract the alpha-proton of the substrate acyl-CoA, suggesting that the C-terminal domain moves to close the active site upon substrate binding. The pyrimidine moiety of flavin is exposed to the solvent and can readily be attacked by molecular oxygen, while that in MCAD is protected from the solvent. The crevice for binding the fatty acyl chain is 28 A long and 6 A wide, large enough to accommodate the C23 acyl chain.

Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase: Effect of Mutations on Enzyme Catalysis

“…In acyl-CoA oxidase, a glycine residue is in the same position as Thr168 in MCAD (51). This gives rise to a situation similar to that of the Thr168Ala mutant of the present study with respect to hydrogen bonding patterns, but with a greater cavity.…”

Structure and DNA binding of alkylation response protein AidB

“…wrote the paper. (19), isovaleryl acyl-CoA dehydrogenase (IVD, PDB ID code 1IVH) (18), acyl-CoA oxidase II (ACO, PDB ID code 1IS2) (9), and nitroalkane oxidase (NAO, PDB ID code 2C0U) (26). AidB residues important for tetramerization and DNA binding are highlighted gray and black, respectively, and those predicted to contact DNA are marked with black triangles.…”

“…In ACADs, the AB/CD dimer interface is formed from helices ␣H and ␣K on domain III. In AidB, this interface is occluded by domain IV, which is a truncated version of that found in the dimeric acyl-CoA oxidase II (ACO) (9) (Fig. 2B).…”

Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms

“…Although the O 2 reactivity of NAO is not a characteristic of its ACD homologs, it is analogous to peroxisomal acyl-CoA oxidase (ACO). ACO is a homodimeric enzyme with an approximately 440 amino-acid Nterminal FAD domain that is structurally homologous to the ACDs (Nakajima et al, 2002), but shares only approximately 7% primary sequence similarity to NAO. Thus, whereas the ACDs transfer reducing equivalents to the electron-transport chain, the ACO and NAO in contrast react with O 2 to complete the reaction cycle (Fitzpatrick, 2001).…”

“…Although no crystal structures are currently available for NAO, structures are available for several NAO homologs, including the fatty acyl-CoA dehydrogenase (ACD) superfamily members rat short-chain ACD (Battaile et al, 2002), Megasphaera elsdenii butyryl-CoA dehydrogenase (Djordjevic et al, 1995), human medium-chain ACD (Lee et al, 1996), human isovaleryl-CoA dehydrogenase (Tiffany et al, 1997), pig liver mitochondria medium-chain ACD (Kim et al, 1993) and the most distant relative, rat liver peroxisomal acylCoA oxidase-II (ACO; Nakajima et al, 2002). To our knowledge, none of the ACD or ACO enzymes will transform nitroalkanes, nor will NAO transform acyl-CoA substrates (Daubner et al, 2002).…”