Crystal Structures of Medium-Chain Acyl-CoA Dehydrogenase from Pig Liver Mitochondria with and Without Substrate

• Published in: Proceedings of the National Academy of Sciences - PNAS 1993-08, Vol.90 (16), p.7523-7527
• Main Authors: Kim, Jung-Ja P., Wang, Ming, Paschke, Rosemary
• Format: Article
• Language: English
• Subjects: Active sites; Acyl-CoA Dehydrogenase; Acyl-CoA Dehydrogenases - chemistry; Acyl-CoA Dehydrogenases - isolation & purification; Acyl-CoA Dehydrogenases - metabolism; Amino Acid Sequence; Analytical, structural and metabolic biochemistry; Animals; Binding Sites; Biochemistry; Biological and medical sciences; Crystalline structure; Crystallization; Crystals; Dehydrogenases; Enzyme substrates; Enzymes; Enzymes and enzyme inhibitors; Flavin-Adenine Dinucleotide - metabolism; Fundamental and applied biological sciences. Psychology; Hogs; Hydrogen Bonding; Hydrogen bonds; Ligands; Mitochondria, Liver - enzymology; Models, Molecular; Molecular biophysics; Molecules; Oxidoreductases; Oxygen; Protein Folding; Protein Structure, Secondary; Structure in molecular biology; Swine; X-Ray Diffraction; X-rays
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.90.16.7523

The three-dimensional structure of medium-chain acyl-CoA dehydrogenase from pig mitochondria in the native form and that of a complex of the enzyme and a substrate (product) have been solved and refined by x-ray crystallographic methods at 2.4-Å resolution to R factors of 0.172 and 0.173, respectively. The overall polypeptide folding and the quaternary structure of the tetramer are essentially unchanged upon binding of the ligand, octanoyl (octenoyl)-CoA. The ligand binds to the enzyme at the rectus (re) face of the FAD in the crevice between the two α-helix domains and the β-sheet domain of the enzyme. The fatty acyl chain of the thioester substrate is buried inside of the polypeptide and the 3'-AMP moiety is close to the surface of the tetrameric enzyme molecule. The alkyl chain displaces the tightly bound water molecules found in the native enzyme and the carbonyl oxygen of the thioester interacts with the ribityl 2'-hydroxyl group of the FAD and the main-chain carbonyl oxygen of Glu-376. The Cα-Cβof the fatty acyl moiety lies between the flavin and the γ-carboxylate of Glu-376, supporting the role of Glu-376 as the base that abstracts the α proton in the α-β dehydrogenation reaction catalyzed by the enzyme. Trp-166 and Met-165 are located at the sinister (si) side of the flavin ring at the surface of the enzyme, suggesting that they might be involved in the interactions with electron transferring flavoprotein. Lys-304, the prevalent mutation site found in patients with medium-chain acyl-CoA dehydrogenase deficiency, is located ≈20 Å away from the active site of the enzyme.