Acyl-CoA oxidase

Fatty acid beta-oxidation forms the 2-trans-enoyl-CoA. Acyl-CoA oxidases (ACXs) in peroxisomes and acyl-CoA dehydrogenases (ACADs) in mitochondria catalyze the rate-limiting step, which showed in Fig. 1. The fatty acids are first activated through thioesterification by acyl-CoA synthetases (ACS). ACXs interact with the FAD cofactor to reduce molecular oxygen in order to convert the acyl-thioester into 2-trans-enoyl-CoA. In the peroxisomal matrix, the H₂O₂ generated from the process can be removed by catalases (CAT). Then, two subsequent enzymatic reactions convert 2-trans-enoyl-CoA to 3-ketoacyl-CoA with the help of multifunctional proteins (MFP). The role of thiolases is to catalyze the substrate for the thiolytic removal of an acetyl-CoA unit.

Fig. 1. The core of the peroxisomal b-oxidation pathway required for oxidation of fatty acids in plants.
(Susan Arent, et al. 2008)

Catalytic Mechanisms

ACXs and ACADs catalyze the rate-limiting step in peroxisomal β-oxidation cycles, using a catalytic glutamate residue to install a double-bond α-β to the CoA-thioester of their substrates, and researchers have studied the α-β dehydrogenation of acyl-CoA. ACXs and ACADs pass the electrons to FAD, molecular oxygen to oxidize the substrates, respectively. Recent studies of RnACX crystallography with fatty acid and ACX4 have revealed the structure of HsVLC-ACAD. The results support that the whole super family uses the same mechanism in the first reaction strongly. By reducing the pKa of the acyl-CoA α-proton, the catalytic base with hydrogen bonds to the backbone nitrogen of the catalytic base which may activate the substrate for deprotonation, while the oxygen atom is sandwiched between the catalytic base and the FAD. FAD reduces the cofactor to FADH and produce the trans-2-enoyl-CoA product while proton transfer to the catalytic base. Some bacterial ACADs have the catalytic base localization swapped to helix G, but mutational and crystallographic studies show that this change is without major effect on catalysis and on the position of the catalytic base relative to flavin. A similar peculiarity is not observed in ACXs, all of which seem to have the catalytic glutamate in the loop between helix J and K. Although some of the ACOX enzymes in C. elegans process both fatty acyl-CoA substrates and ascaroside CoA substrates, others are specialized for processing only specific ascaroside-CoA substrates.

Structure

ACXs contains about 650 amino acid residues, and a few difference existed among different species. The crystal structure of ACXs were studied in many species, including rice, rat, human, Arabidopsis, soybean and so on. A lot of structurally related enzymes which existed in most organisms showing that they can catalyze a double bond between the C2 and C3 position of fatty acid CoA thioesters. ACXs are the incidental products during the first step of activating the C3 position for the nucleophile attack needed for the subsequent thiolytic degradation of amino acids, fatty acids, tryptophan and lysine, and for the synthesis of polyketides. The overall structure of ACXs showed that different types have a few difference, while each structure consisting of at least three domains: a helical N-terminal domain, a central b-sheet domain, and a helical C-terminal domain, which defines the ACAD-like superfamily. In the minimal structure, the superfamily name refers to the mammalian mitochondrial enzyme.

Substrate Specificity

The acyl-CoA-binding pocket of dimeric ACAD-like enzymes is visualized in the crystal structures of RnACX and HsVLC-ACAD with acyl chains in the active site. The substrate specificity of ACXs have some relation with the static snapshots of an averaged dynamic protein system, which provide essential information on substrate interactions. In the solvent accessible acyl-binding pocket, there seems to be no limit to the length of the acyl chain. This means that these enzymes have evolved to be specific for the longer chain substrates rather than the smaller chain substrates and the notion correlates well with the fact. But a few confusion existed still because it does not explain why ACX1-3s in plant species do not have uniform substrate profiles or why SC-CoAs are poor substrates. The size and shape of the HsVLC-ACAD and AtACX1 acyl-binding pocket varies can be seen in Fig. 2. During the JA-CoA biosynthesis, the plant ACX1 plays a very important role. The JA-CoA precursor OPC-8:0-CoA is a flat bulky substrate when compared with acyl-CoA and would be expected to require a more spacious binding pocket than acyl-substrates. The AtACX1 pocket is indeed more spacious than the binding pocket of HsVLC-ACAD (8*12 Å versus 8*8 Å width of the channel).

Fig. 2. Acyl-CoA-binding pockets (Susan Arent, et al. 2008)

References

1. Susan Arent, Valerie E. Pye, Anette Henriksen. Structure and function of plant acyl-CoA oxidases. Plant Physiology and Biochemistry, 46 (2008) 292-301.
2. Xinxing Zhang. et al. Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. PNAS, 2016, 113(36) 10055–10060.