L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study

Paul LanganAndrey Kovalevsky


D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that the mechanism of ring-opening is the same as for the reaction with D-xylose. Structural evidence and QM/MM calculations show that in the reactive Michaelis complex L-arabinose is distorted to the high-energy (5)S1 conformation; this may explain the apparent high KM for this sugar. MD-FEP simulations indicate that amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose were found in furanose forms when bound to XI. We propose that these complexes containing Ni(2+) cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism.


Dec 8, 1992·Biochemistry·C A CollyerP Grice
Jun 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·H L CarrellJ F Biellmann
Mar 16, 1971·Biochemistry·K J Schray, I A Rose
Jan 1, 1983·Acta Chemica Scandinavica. Series B: Organic Chemistry and Biochemistry·K BockL Wiebe
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyKlaus Schulten
Jan 11, 2001·Biochimica Et Biophysica Acta·B S HartleyM Rangarajan
Feb 17, 2001·Biotechnology and Bioengineering·Matti LeisolaOssi Pastinen
Jun 5, 2002·Chemical & Pharmaceutical Bulletin·Masao AkagiHidehito Urata
Oct 10, 2002·Current Protein & Peptide Science·B Asbóth, G Náray-Szabó
Dec 24, 2002·Journal of Computational Chemistry·Mireia Garcia-VilocaJiali Gao
Mar 1, 1994·Acta Crystallographica. Section D, Biological Crystallography·H L CarrellJenny P Glusker
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
May 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Amy K KatzGerard J Bunick
Oct 13, 2006·Antonie van Leeuwenhoek·Antonius J A van MarisJack T Pronk
Jan 20, 2009·Applied Microbiology and Biotechnology·M HelantoA Nyyssölä
May 26, 2009·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPaul Langan
Aug 29, 2009·Bioprocess and Biosystems Engineering·Young-Ju JeonIn-Ho Kim
Feb 4, 2010·Biochimica Et Biophysica Acta·Kosei TakedaShigehiro Kamitori
Aug 30, 2011·Applied Microbiology and Biotechnology·Chao HuCuiying Hu
May 16, 2012·Protein Engineering, Design & Selection : PEDS·Darshan H PatelHyeun-Jong Bae
Sep 6, 2012·Acta Crystallographica. Section D, Biological Crystallography·Andrey KovalevskyPaul Langan
Jan 10, 2014·Protein Engineering, Design & Selection : PEDS·Mary Jo WaltmanAndrey Kovalevsky
Feb 18, 2014·Acta Crystallographica. Section D, Biological Crystallography·Parthapratim MunshiFlora Meilleur


Mar 31, 2015·Journal of Molecular Biology·Christian Edlich-MuthErnest D Laue
Nov 25, 2015·Archives of Biochemistry and Biophysics·William B O'DellFlora Meilleur
Jun 16, 2016·Acta Crystallographica. Section F, Structural Biology Communications·Mirja KrauseRik K Wierenga
Jul 3, 2016·Applied Microbiology and Biotechnology·Hiromi YoshidaShigehiro Kamitori
Apr 20, 2018·Emerging Topics in Life Sciences·Matthew P Blakeley, Alberto D Podjarny

Related Concepts

Glucose isomerase
Bacterial Proteins
Plasma Protein Binding Capacity
Molecular Stereochemistry
Crystallography, X-Ray

Trending Feeds


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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Lipidomics & Rhinovirus Infection

Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

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.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

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.

Laryngeal Neoplasms

Laryngeal Neoplasms occur in the Larynx and are typically associated with smoking and alcohol consumption. Discover the latest research on Laryngeal Neoplasms here.

Cell Atlas Along the Gut-Brain Axis

Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here.