Journal ArticleDOI
Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant
Parthapratim Munshi,Edward H. Snell,Mark J. van der Woerd,Russell A. Judge,Dean A. A. Myles,Zhong Ren,Flora Meilleur +6 more
TLDR
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 and 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.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.read more
Citations
More filters
Journal ArticleDOI
Neutron protein crystallography: A complementary tool for locating hydrogens in proteins
TL;DR: Methods to produce isotopically-substituted proteins and to grow large crystals are provided in the context of neutron structures reported in the literature along with technique-specific strategies including joint X-ray/neutron structure refinement.
Journal ArticleDOI
Operando Solid-State NMR Observation of Solvent-Mediated Adsorption-Reaction of Carbohydrates in Zeolites
Long Qi,Ricardo Alamillo,William A. Elliott,Amity Andersen,David W. Hoyt,Eric D. Walter,Kee Sung Han,Nancy M. Washton,Robert M. Rioux,James A. Dumesic,Susannah L. Scott +10 more
TL;DR: In this paper, the origin of the complex solvent effect using operando solid-state NMR spectroscopy was elucidated using operandando solid state NMR (OSNMR) spectrograms.
Journal ArticleDOI
Neutron scattering in the biological sciences: progress and prospects
Rana Ashkar,Hassina Z. Bilheux,Heliosa Bordallo,Robert M. Briber,David J.E. Callaway,Xiaolin Cheng,Xiang-Qiang Chu,Joseph E. Curtis,Mark Dadmun,Paul W. Fenimore,David Fushman,Frank Gabel,Kushol Gupta,Frederick Herberle,Frank Heinrich,Frank Heinrich,Liang Hong,John Katsaras,John Katsaras,Zvi Kelman,Eugenia Kharlampieva,Gerald R. Kneller,Andrey Kovalevsky,Susan Krueger,Paul Langan,Raquel L. Lieberman,Yun Liu,Mathias Lösche,Edward Lyman,Yimin Mao,John P. Marino,Carla Mattos,Flora Meilleur,Flora Meilleur,Peter C. E. Moody,Jonathan D. Nickels,William B. O'Dell,Hugh O'Neill,Ursula Perez-Salas,Judith Peters,Loukas Petridis,Alexei P. Sokolov,Christopher B. Stanley,Norman Wagner,Michael Weinrich,Kevin L. Weiss,Troy Wymore,Yang Zhang,Jeremy C. Smith +48 more
TL;DR: Crystallography, solution scattering, dynamics, membranes, labeling and imaging, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods are examined.
Journal ArticleDOI
Catalyst characterization in the presence of solvent: development of liquid phase structure-activity relationships.
Nicholas S. Gould,Bingjun Xu +1 more
TL;DR: Due to the low volatility and highly oxygenated nature of biomass derived feedstocks, biomass upgrade reactions are frequently conducted in the presence of solvent to improve substrate mass transfer to the catalyst surface.
Journal ArticleDOI
L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.
Paul Langan,Amandeep K. Sangha,Troy Wymore,Jerry M. Parks,Zamin Koo Yang,B. Leif Hanson,Zoë Fisher,Sax A. Mason,Matthew P. Blakeley,V. Trevor Forsyth,Jenny P. Glusker,H. L. Carrell,Jeremy C. Smith,Jeremy C. Smith,David A. Keen,David E. Graham,Andrey Kovalevsky +16 more
TL;DR: X-ray and neutron crystallographic studies are presented to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L- ribulose and L-ribose, respectively and it is proposed that these complexes containing Ni(2+) cofactors are Michaelis-like and the isomersization between these two sugars proceeds via a cis-ene-diol mechanism.
References
More filters
Journal ArticleDOI
Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Journal ArticleDOI
Overview of the CCP4 suite and current developments.
Martyn Winn,Charles Ballard,Kevin Cowtan,Eleanor J. Dodson,Paul Emsley,Phil Evans,Ronan M. Keegan,Eugene Krissinel,Andrew G. W. Leslie,Airlie J. McCoy,Stuart McNicholas,Garib N. Murshudov,Navraj S. Pannu,E. Potterton,Harold R. Powell,Randy J. Read,Alexei A. Vagin,Keith S. Wilson +17 more
TL;DR: An overview of the CCP4 software suite for macromolecular crystallography is given.
Journal ArticleDOI
PHENIX: building new software for automated crystallographic structure determination
Paul D. Adams,Ralf W. Grosse-Kunstleve,Li-Wei Hung,Thomas R. Ioerger,Airlie J. McCoy,Nigel W. Moriarty,Randy J. Read,James C. Sacchettini,Nicholas K. Sauter,Thomas C. Terwilliger +9 more
TL;DR: A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is developed, which will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.
Journal ArticleDOI
X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator
H. L. Carrell,Jenny P. Glusker,Vincent Burger,Franco Manfre,Denis Tritsch,Jean-François Biellmann +5 more
TL;DR: The changes in structure of the native enzyme, the enzyme with bound substrate, and the alkylated enzyme indicate that the mechanism involves an "open-chain" conformation of substrate and that the intermediate in the isomerization reaction is probably a cis-ene diol because the active-site histidine is correctly placed to abstract a proton from C1 or C2 of the substrate.