9YD7
Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate
Summary for 9YD7
| Entry DOI | 10.2210/pdb9yd7/pdb |
| Descriptor | Dihydroorotase, N-CARBAMOYL-L-ASPARTATE, ZINC ION, ... (4 entities in total) |
| Functional Keywords | hydrolase, complex, dihydroorotase, tim barrel |
| Biological source | Methanocaldococcus jannaschii |
| Total number of polymer chains | 1 |
| Total formula weight | 49121.65 |
| Authors | Vitali, J.,Nix, J.C.,Newman, H.E.,Colaneri, M.J. (deposition date: 2025-09-22, release date: 2025-12-17) |
| Primary citation | Vitali, J.,Nix, J.C.,Newman, H.E.,Colaneri, M.J. Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound. Acta Crystallogr.,Sect.F, 2026 Cited by PubMed Abstract: Here, we report the X-ray structural analysis of dihydroorotase from Methanococcus jannaschii co-crystallized with dihydroorotate at pH 6.5. The crystals are isomorphous with the crystals of the apoenzyme, with space group P321 and unit-cell dimensions a = b = 111.4, c = 101.2 Å. The structure was refined to R = 0.169 and R = 0.186 at a resolution of 1.87 Å at room temperature. During crystallization the degradative reaction took place, and the electron density in the active site corresponds to the substrate carbamoyl aspartate. Carbamoyl aspartate interacts with the protein in the active site in a manner similar to that observed for Escherichia coli and human dihydroorotases. However, the flexible loop (residues 140-151) adopts both conformations in the crystal, loop-out and loop-in, with the loop-out conformation having higher occupancy. This contrasts with our expectations for the flexible loop to be exclusively in the loop-in conformation, which is the conformation that it adopts to stabilize the binding of the substrate in the known systems. Additional studies with substrate analogs that resemble carbamoyl aspartate and different crystallization conditions would provide further insight into the conformation of the flexible loop in this system. PubMed: 41355244DOI: 10.1107/S2053230X25010556 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.87 Å) |
Structure validation
Download full validation report
