X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis

A LavieDagmar Ringe


The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the interconversion between glucose and fructose (xylose and xylulose under physiological conditions) by utilizing two metal cofactors to promote a hydride shift; the metals are bridged by a glutamate residue. This puts xylose isomerase in the small but rapidly growing family of enzymes with a bridged bimetallic active site, in which both metals are involved in the chemical transformation. The substrate 3-O-methylglucose was chosen in order to position the glucose molecule in the observed electron density unambiguously. Of the two essential magnesium ions per active site, Mg-2 was observed to occupy two alternate positions, separated by 1.8 A, in the substrate-soaked structures. The deduced movement was not observed in the structure without substrate present and is attributed to a step following substrate binding but prior to isomerization. The substrates glucose and 3-O-methylgluc...Continue Reading


Dec 24, 2002·Journal of Computational Chemistry·Mireia Garcia-VilocaJiali Gao
Nov 30, 2011·European Biophysics Journal : EBJ·John W BradyAttilio Cesàro
Nov 5, 2003·Journal of Molecular Biology·Ashish V TendulkarChetan Y Mone
Jan 1, 1997·Progress in Biophysics and Molecular Biology·C S Sundari, D Balasubramanian
Nov 14, 1997·International Journal of Biological Macromolecules·S Janecek
Feb 19, 2000·Current Opinion in Chemical Biology·Gregory A Petsko, Dagmar Ringe
Feb 10, 2009·Journal of the American Chemical Society·J Javier Ruiz-PerníaIñaki Tuñón
Sep 6, 2012·Acta Crystallographica. Section D, Biological Crystallography·Andrey Y KovalevskyPaul Langan
Oct 9, 2013·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Jea-Won ChoByung Il Lee
Mar 26, 1999·Protein Science : a Publication of the Protein Society·A TeplyakovB Badet
Apr 25, 2002·Annual Review of Physical Chemistry·Jiali Gao, Donald G Truhlar
Feb 18, 2014·Acta Crystallographica. Section D, Biological Crystallography·Parthapratim MunshiFlora Meilleur
May 13, 1999·Proceedings of the National Academy of Sciences of the United States of America·Y J SunC D Hsiao
Oct 19, 2001·Proceedings of the National Academy of Sciences of the United States of America·M J OndrechenDagmar Ringe
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Diana ArsenievaConstance J Jeffery
May 5, 2006·European Biophysics Journal : EBJ·Flora MeilleurDean A A Myles
Feb 13, 2016·Journal of Molecular Biology·Wouter G TouwG Vriend
Apr 26, 2008·Journal of Molecular Biology·Cong LiuXiao-Dong Su
Aug 24, 2004·Protein Science : a Publication of the Protein Society·Mireia Garcia-VilocaJiali Gao
Oct 20, 2005·Magnetic Resonance in Chemistry : MRC·R KapplJ Hüttermann
Mar 21, 2008·Carbohydrate Research·K Buchholz, J Seibel
Jan 16, 2013·Journal of Molecular Biology·Moshe Ben-DavidDan S Tawfik
Mar 5, 1999·Journal of Molecular Biology·A Kasuya, J M Thornton
Jul 6, 2019·Journal of Synchrotron Radiation·Helena TabermanElspeth F Garman
Sep 29, 1995·The Journal of Biological Chemistry·R D WhitakerC A Batt
Sep 19, 2019·Nature Methods·Pedram MehrabiR J Dwayne Miller
Feb 17, 2017·Bioinformatics·P P WozniakM Kotulska
Jun 11, 2004·The Journal of Biological Chemistry·María J Maté, Colin Kleanthous

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