title: L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.
abstract: 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.
authors.affiliation: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Langan
authors.affiliation: UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Amandeep K
authors.initials: AK
authors.lastname: Sangha
authors.affiliation: UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Troy
authors.initials: T
authors.lastname: Wymore
authors.affiliation: UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Jerry M
authors.initials: JM
authors.lastname: Parks
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Zamin Koo
authors.initials: ZK
authors.lastname: Yang
authors.affiliation: Chemistry Department, University of Toledo, Toledo, OH 43606, USA.
authors.forename: B Leif
authors.initials: BL
authors.lastname: Hanson
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Zoe
authors.initials: Z
authors.lastname: Fisher
authors.affiliation: Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.
authors.forename: Sax A
authors.initials: SA
authors.lastname: Mason
authors.affiliation: Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Blakeley
authors.affiliation: Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France; EPSAM/ISTM, Keele University, Staffordshire ST5 5BG, UK.
authors.forename: V Trevor
authors.initials: VT
authors.lastname: Forsyth
authors.affiliation: Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
authors.forename: Jenny P
authors.initials: JP
authors.lastname: Glusker
authors.affiliation: Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
authors.forename: Horace L
authors.initials: HL
authors.lastname: Carrell
authors.affiliation: 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.
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.affiliation: ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, Oxon, England.
authors.forename: David A
authors.initials: DA
authors.lastname: Keen
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Graham
authors.affiliation: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. Electronic address: kovalevskyay@ornl.gov.
authors.forename: Andrey
authors.initials: A
authors.lastname: Kovalevsky
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000737:chemistry*; D001089:Arabinose / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D055162:Biocatalysis; D002104:Cadmium / Q000737:chemistry; D018360:Crystallography, X-Ray; D008274:Magnesium / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D013237:Stereoisomerism; D013302:Streptomyces / Q000201:enzymology; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D002104:Cadmium; D001089:Arabinose; D019747:Aldose-Ketose Isomerases; C023298:xylose isomerase; D008274:Magnesium