D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimeri ...
D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that the mechanism of ring-opening is the same as for the reaction with D-xylose. Structural evidence and QM/MM calculations show that in the reactive Michaelis complex L-arabinose is distorted to the high-energy (5)S1 conformation; this may explain the apparent high KM for this sugar. MD-FEP simulations indicate that amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose were found in furanose forms when bound to XI. We propose that these complexes containing Ni(2+) cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism.
Organizational Affiliation:
Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.,Chemistry Department, University of Toledo, Toledo, OH 43606, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. Electronic address: kovalevskyay@ornl.gov.,Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.,Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France; EPSAM/ISTM, Keele University, Staffordshire ST5 5BG, UK.,ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, Oxon, England.
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