9WIC
Crystal structure of the human dihydroorotase domain complexed with 5-aminoorotic acid reveals the loop in binding mode
Summary for 9WIC
| Entry DOI | 10.2210/pdb9wic/pdb |
| Descriptor | CAD protein, 5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid, ZINC ION, ... (4 entities in total) |
| Functional Keywords | dihydroorotase, human cad, hydrolase, zn |
| Biological source | Homo sapiens (human) |
| Total number of polymer chains | 1 |
| Total formula weight | 43063.78 |
| Authors | |
| Primary citation | Huang, Y.H.,Huang, T.Y.,Wang, M.C.,Huang, C.Y. Structural basis of potent inhibition of the human CAD dihydroorotase domain by 5-aminoorotic acid. Biochem.Biophys.Res.Commun., 787:152804-152804, 2025 Cited by PubMed Abstract: Dihydroorotase (DHOase) catalyzes the reversible conversion of N-carbamoyl-L-aspartate to dihydroorotate in de novo pyrimidine biosynthesis. In humans, DHOase (huDHOase) is part of the CAD enzyme complex and contains a flexible loop that alternates between loop-in and loop-out conformations. Here, we identify 5-aminoorotic acid (5-AOA), previously known as a dihydroorotate dehydrogenase inhibitor, as a potent huDHOase inhibitor. Enzyme assays showed strong inhibition by 5-AOA (IC = 9.87 μM) compared with weaker inhibition by 5-fluoroorotic acid (5-FOA; IC = 191.59 μM). To elucidate the mechanism, we determined the crystal structures of huDHOase bound to 5-AOA (1.83 Å; PDB ID: 9WIC) and to 5-FOA (1.55 Å; PDB ID: 9WIN) for direct comparison. Structural analysis revealed distinct binding modes: 5-AOA bound in the loop-in conformation, forming extensive stabilizing interactions, whereas 5-FOA bound in the loop-out state with fewer contacts. Consistently, the T1562A mutation decreased the binding affinity of 5-AOA from 18.6 μM to 53.4 μM, an approximately threefold reduction, confirming the role of the loop in inhibitor recognition. These findings establish 5-AOA as a dual inhibitor in pyrimidine biosynthesis and highlight a loop-in binding mechanism for huDHOase inhibition. PubMed: 41101239DOI: 10.1016/j.bbrc.2025.152804 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.83 Å) |
Structure validation
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