Inhibition of d-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography

Journal Article · Sat Sep 01 04:00:00 EDT 2012 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S0907444912024808· OSTI ID:22351271

Kovalevsky, Andrey ^[1]; Hanson, B. Leif ^[2]; Mason, Sax A. ^[3]; Forsyth, V. Trevor ^[3]; Fisher, Zoe ^[1]; Mustyakimov, Marat ^[1]; Blakeley, Matthew P. ^[3]; Keen, David A. ^[4]; Langan, Paul ^[5]

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1. Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545 (United States)
2. University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606 (United States)
3. Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France)
4. Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (United Kingdom)
5. Oak Ridge National Laboratory, PO Box 2008, MS 6475, Oak Ridge, TN 37831 (United States)

A joint X-ray/neutron structure of d-xylose isomerase in complex with the inhibitor sorbitol was determined at room temperature at an acidic pH of 5.9. Protonation of the O5 O atom of the sugar was directly observed in the nuclear density maps. Under acidic conditions sorbitol gains a water-mediated interaction with the enzyme active site, which may explain the increased potency of the inhibitor at low pH. d-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni{sup 2+} cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg{sup 2+} ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni{sup 2+} ions occupying the catalytic metal site (M2) were found at two locations, while Mg{sup 2+} in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.

• OSTI ID: 22351271
• Journal Information: Acta Crystallographica. Section D: Biological Crystallography, Journal Name: Acta Crystallographica. Section D: Biological Crystallography Journal Issue: Pt 9 Vol. 68; ISSN ABCRE6; ISSN 0907-4449
• Country of Publication: Denmark
• Language: English

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
AFFINITY
ATOMS
CRYSTALLOGRAPHY
DENSITY
GLUCOSE
HYDRATION
INTERACTIONS
METALS
NEUTRONS
NUCLEAR MATTER
OXYGEN
RESOLUTION
SACCHAROSE
WATER