L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study

• Published in: Structure (London) 2014-09, Vol.22 (9), p.1287-1300
• Main Authors: Langan, Paul, Sangha, Amandeep K., Wymore, Troy, Parks, Jerry M., Yang, Zamin Koo, Hanson, B. Leif, Fisher, Zoe, Mason, Sax A., Blakeley, Matthew P., Forsyth, V. Trevor, Glusker, Jenny P., Carrell, Horace L., Smith, Jeremy C., Keen, David A., Graham, David E., Kovalevsky, Andrey
• Format: Article
• Language: English
• Subjects: Aldose-Ketose Isomerases - chemistry; Arabinose - chemistry; Bacterial Proteins - chemistry; Biocatalysis; Cadmium - chemistry; Crystallography, X-Ray; Magnesium - chemistry; Molecular Dynamics Simulation; Protein Binding; Stereoisomerism; Streptomyces - enzymology; Thermodynamics
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2014.07.002

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 5S1 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 Ni2+ cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism. [Display omitted] •Joint X-ray/neutron structures of D-xylose isomerase with L-arabinose•Structures and QM/MM reveal L-arabinose conformation is 5S1 in the active site•MD simulations suggest mutations to improve enzyme affinity to L-arabinose•Isomerization between L-ribulose and L-ribose may proceed by cis-ene-diol pathway Using X-ray/neutron crystallography and QM/MM, Langan et al. show that L-arabinose has a high-energy 5S1 conformation in complex with reactive D-xylose isomerase. They propose that L-arabinose isomerizes through hydride shift, whereas isomerization between L-ribulose and L-ribose may involve a cis-ene-diol.