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

Biochemistry
A LavieDagmar Ringe

Abstract

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

Citations

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

Related Concepts

Glucose isomerase
DNA Sequence
Carbohydrate Epimerases
Catalysis
Levulosa Ife
Anhydrous Dextrose
Magnesium
Methylglucosides
Solvents
Streptomyces

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.