Catalyzes the conversion of isovaleryl-CoA/3-methylbutanoyl-CoA to 3-methylbut-2-enoyl-CoA as an intermediate step in the leucine (Leu) catabolic pathway. To a lesser extent, is also able to catalyze the oxidation of other saturated short-chain acyl-CoA thioesters as pentanoyl-CoA, hexenoyl-CoA and butenoyl-CoA. 3-methylbutanoyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = 3-methyl-(2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + oxidized [electron-transfer flavoprotein] + pentanoyl-CoA = (2E)-pentenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + hexanoyl-CoA + oxidized [electron-transfer flavoprotein] = (2E)-hexenoyl-CoA + reduced [electron-transfer flavoprotein] butanoyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = (2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein] Amino-acid degradation; L-leucine degradation; (S)-3-hydroxy-3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 1/3. Homotetramer. Belongs to the acyl-CoA dehydrogenase family.