Involved in the initial and rate-limiting step of peroxisomal beta-oxidation of straight-chain saturated and unsaturated very-long-chain fatty acids. Catalyzes the desaturation of fatty acyl-CoAs such as palmitoyl-CoA (hexadecanoyl-CoA) to 2-trans-enoyl-CoAs ((2E)-enoyl-CoAs) such as (2E)-hexadecenoyl-CoA, and donates electrons directly to molecular oxygen (O(2)), thereby producing hydrogen peroxide (H(2)O(2)). Shows highest activity against medium-chain fatty acyl-CoAs. Shows optimum activity with a chain length of 10 carbons (decanoyl-CoA) in vitro. Is active against a much broader range of substrates and shows activity towards long-chain acyl-CoAs. a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2 hexadecanoyl-CoA + O2 = (2E)-hexadecenoyl-CoA + H2O2 dodecanoyl-CoA + O2 = (2E)-dodecenoyl-CoA + H2O2 O2 + octanoyl-CoA = (2E)-octenoyl-CoA + H2O2 decanoyl-CoA + O2 = (2E)-decenoyl-CoA + H2O2 O2 + tetradecanoyl-CoA = (2E)-tetradecenoyl-CoA + H2O2 hexadecanedioyl-CoA + O2 = (2E)-hexadecenedioyl-CoA + H2O2 O2 + tetracosanoyl-CoA = (2E)-tetracosenoyl-CoA + H2O2 glutaryl-CoA + O2 = (2E)-glutaconyl-CoA + H2O2 hexanoyl-CoA + O2 = (2E)-hexenoyl-CoA + H2O2 O2 + octadecanoyl-CoA = (2E)-octadecenoyl-CoA + H2O2 (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA + O2 = (2E,5Z,8Z,11Z,14Z,17Z)-icosahexaenoyl-CoA + H2O2 (6Z,9Z,12Z,15Z,18Z,21Z)-tetracosahexaenoyl-CoA + O2 = (2E,6Z,9Z,12Z,15Z,18Z,21Z)-tetracosaheptaenoyl-CoA + H2O2 Lipid metabolism; peroxisomal fatty acid beta-oxidation. Homodimer (By similarity). Interacts with LONP2 (By similarity). Highest levels of isoform 1 are found in liver and kidney while highest levels of isoform 2 are found in white adipose tissue. Isoform 1 is expressed at higher levels than isoform 2 in liver and kidney while isoform 2 is expressed at higher levels in brain, heart, lung, muscle, white adipose tissue and testis. Severe microvesicular hepatic steatosis, sustained activation of Ppara, spontaneous massive peroxisome proliferation and eventual development of hepatocellular carcinomas (PubMed:20195242). Null mice have strikingly increased levels of both n-3 and n-6 very long chain polyunsaturated fatty acids (over twenty-four (24) carbons long) (PubMed:11855929). Belongs to the acyl-CoA oxidase family. Truncated N-terminus.