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Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant.

Munshi P, Snell EH, van der Woerd MJ, Judge RA, Myles DA, Ren Z, Meilleur F
Acta Crystallogr D Biol Crystallogr 70 414-20 (2014)
Cited: 9 times
EuropePMC logo PMID: 24531475

Abstract

Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl group via an activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.

Reviews - 4lnc mentioned but not cited (1)

  1. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD. Acta Crystallogr D Struct Biol 74 800-813 (2018)

Articles - 4lnc mentioned but not cited (1)

  1. Large-volume protein crystal growth for neutron macromolecular crystallography. Ng JD, Baird JK, Coates L, Garcia-Ruiz JM, Hodge TA, Huang S. Acta Crystallogr F Struct Biol Commun 71 358-370 (2015)


Reviews citing this publication (3)

  1. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. O'Dell WB, Bodenheimer AM, Meilleur F. Arch Biochem Biophys 602 48-60 (2016)
  2. Catalyst characterization in the presence of solvent: development of liquid phase structure-activity relationships. Gould NS, Xu B. Chem Sci 9 281-287 (2018)
  3. The use of neutron scattering to determine the functional structure of glycoside hydrolase. Nakamura A, Ishida T, Samejima M, Igarashi K. Curr Opin Struct Biol 40 54-61 (2016)

Articles citing this publication (4)

  1. Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. Taberman H, Bury CS, van der Woerd MJ, Snell EH, Garman EF. J Synchrotron Radiat 26 931-944 (2019)
  2. L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study. Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, Kovalevsky A. Structure 22 1287-1300 (2014)
  3. X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates. Yoshida H, Yoshihara A, Ishii T, Izumori K, Kamitori S. Appl Microbiol Biotechnol 100 10403-10415 (2016)
  4. Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways. Hermann J, Nowotny P, Schrader TE, Biggel P, Hekmat D, Weuster-Botz D. Acta Crystallogr F Struct Biol Commun 74 754-764 (2018)


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