Selenomethionine substitution of orotidine-5′-­monophosphate decarboxylase causes a change in crystal contacts and space group

Orotidine 5′-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5′-monophosphate to uridine 5′-monophosphate, the last step in the de novo biosynthesis of uridine 5′-monophosphate. In order to determine the structure of ODCase from Escherichia coli by the multi-wavelength anomalous dispersion technique, both native and SeMet-substituted proteins have been produced and purified. During the production of SeMet ODCase, it was observed that SeMet was the only amino acid that it was necessary to add to the defined medium during expression. SeMet-substituted ODCase in complex with the inhibitor 1-­(5′-phospho-β-­D-­ribofuranosyl)barbituric acid crystallizes under similar conditions as the native enzyme. In contrast to the native enzyme, where the crystals belong to the orthorhombic space group P2₁2₁2₁, the SeMet-substituted enzyme crystallizes in the monoclinic space group P2₁, with a quadrupling of the volume of the asymmetric unit. Despite the drastic difference in symmetry, the overall crystal packing is effectively identical in the two crystal forms. The change in space group appears to originate in differences in the crystal contacts near the SeMet and Met residues. These differences can be rationalized in terms of SeMet's larger size and hydrophobicity.