Extended Data Fig. 8: Structure of human OMPDC in complex with transition-state analog 6-aza-UMP. | Nature Catalysis

Extended Data Fig. 8: Structure of human OMPDC in complex with transition-state analog 6-aza-UMP.

From: Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5′-monophosphate decarboxylase catalysis

Extended Data Fig. 8

Structure of human OMPDC in complex with transition-state analog 6-aza-UMP. (a) Close-up of the active site showing the bound analog, interacting protein groups and water molecules (W). Hydrogen bonds and the bond lengths of the C2-O2 and C4-O4 bonds are indicated. Note the syn-conformation of the base that places the 2-oxo group into the vicinity of the catalytic tetrad rather than Gln430 as observed for all other ligands, which bind in the anti-conformation (see panel b). The structural models are superposed with the corresponding 2mFo-DFc electron density maps at a contour level of 5.3σ (in blue). Crystallographic statistics are provided in Supplementary Table 1. (b) Structural superposition of OMPDC in complex with 6-aza-UMP (in yellow) and UMP (in grey) showing the active site including the bound ligand and selected active site residues. Note the different orientation of the the 2-oxo function for both ligands. Abbreviations: OMPDC, orotidine-5’-monophosphate decarboxylase; UMP, uridine-5’-monophosphate.

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