5Y9D
Crystal structure of acyl-coA oxidase1 from Yarrowia lipolytica
Summary for 5Y9D
| Entry DOI | 10.2210/pdb5y9d/pdb |
| Descriptor | Acyl-coenzyme A oxidase 1, FLAVIN-ADENINE DINUCLEOTIDE (3 entities in total) |
| Functional Keywords | fad-binding protein, oxidoreductase |
| Biological source | Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) |
| Cellular location | Peroxisome : O74934 |
| Total number of polymer chains | 2 |
| Total formula weight | 160662.98 |
| Authors | Kim, S.,Kim, K.-J. (deposition date: 2017-08-24, release date: 2018-01-03, Last modification date: 2023-11-22) |
| Primary citation | Kim, S.,Kim, K.J. Structural insight into the substrate specificity of acyl-CoA oxidase1 from Yarrowia lipolytica for short-chain dicarboxylyl-CoAs. Biochem. Biophys. Res. Commun., 495:1628-1634, 2018 Cited by PubMed Abstract: Acyl-CoA oxidase (ACOX) plays an important role in fatty acid degradation. The enzyme catalyzes the first reaction in peroxisomal fatty acid β-oxidation by reducing acyl-CoA to 2-trans-enoyl-CoA. The yeast Yarrowia lipolytica is able to utilize fatty acids, fats, and oil as carbon sources to produce valuable bioproducts. We determined the crystal structure of ACOX1 from Y. lipolytica (YlACOX1) at a resolution of 2.5 Å. YlACOX1 forms a homodimer, and the monomeric structure is composed of four domains, the Nα, Nβ, Cα1, and Cα2. The FAD cofactor is bound at the dimerization interface between the Nβ- and Cα1-domains. The substrate-binding tunnel formed by the interface between the Nα-, Nβ-, and Cα1-domains is located proximal to FAD. Amino acid and structural comparisons of YlACOX1 with other ACOXs show that the substrate-binding pocket of YlACOX1 is much smaller than that of the medium- or long-chain ACOXs but is rather similar to that of the short-chain ACOXs. Moreover, the hydrophilicity of residues constituting the end region of the substrate-binding pocket in YlACOX1 is quite similar to those in the short-chain ACOXs but different from those of the medium- or long-chain ACOXs. These observations provide structural insights how YlACOX1 prefers short-chain dicarboxylyl-CoAs as a substrate. PubMed: 29198706DOI: 10.1016/j.bbrc.2017.11.191 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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