Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis

Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O(2) to de­hydro­isourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hy­droxy­isourate (5HIU). At different stages of the reaction both catalytic O(2) and water occupy the ‘peroxo hole’ above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H(2)O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O—H⋯π interaction with 8AZA. The active site Lys10–Thr57 dyad features a charged Lys10–NH(3) (+) side chain engaged in a strong hydrogen bond with Thr57(OG1), while the Thr57(OG1–HG1) bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHU(C5) with Thr57(HG1) central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O(2) exchange during catalysis.