PT - JOURNAL ARTICLE AU - Matt Challacombe AU - Nicolas Bock AU - Paul Langan AU - Andrey Kovalevsky TI - Hydroxide Once or Twice? A Combined Neutron Crystallographic and Quantum Chemical Study of the Hydride Shift in D-Xylose Isomerase AID - 10.1101/030601 DP - 2015 Jan 01 TA - bioRxiv PG - 030601 4099 - http://biorxiv.org/content/early/2015/11/04/030601.short 4100 - http://biorxiv.org/content/early/2015/11/04/030601.full AB - We present quantum chemical calculations, through 6-311G**/B3LYP, for the isomerization step in D-Xylose Isomerase, based on truncated models of the 3KCO (linear) and 3KCL (cyclic) X-ray/neutron structures, containing 9 free waters, 2 metals, the sugar and roughly 19 amino acids. Perturbative relaxations upon the experimental framework suggest a possible seven-step mechanism of the isomerzation reaction involving direct ionization of the glucose O2 proton on movement of the mobile magnesium ion (Mg2A → 2B). In this model, we also find a compensating proton shift between the K183/D255 pair, corresponding to a 10kcal/mol reduction in the cost of the ionization, with a delocalized shift in potential along the reaction plane. We find ~16 kcal/mol reaction barriers in reasonable agreement with experiment (14 kcal/mol), as well as a final, exothermic hydroxide consistent with the 3CWH (product) structure, and possibly explaining observed non-Michaelis behavior of this enzyme.