4QE4

Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribulose

Summary for 4QE4

• Entry DOI: 10.2210/pdb4qe4/pdb
• Related: 4QDP 4QDW 4QE1 4QE5 4QEE 4QEH
• Descriptor: Xylose isomerase, NICKEL (II) ION, beta-L-ribulofuranose, ... (4 entities in total)
• Functional Keywords: tim barrel, sugar isomerase, monosaccharides, isomerase
• Biological source: Streptomyces rubiginosus
• Cellular location: Cytoplasm: P24300
• Total number of polymer chains: 1
• Total formula weight: 43550.81

Authors

Kovalevsky, A.Y.,Langan, P. (deposition date: 2014-05-15, release date: 2014-09-03, Last modification date: 2024-02-28)

Primary citation

Langan, P.,Sangha, A.K.,Wymore, T.,Parks, J.M.,Yang, Z.K.,Hanson, B.L.,Fisher, Z.,Mason, S.A.,Blakeley, M.P.,Forsyth, V.T.,Glusker, J.P.,Carrell, H.L.,Smith, J.C.,Keen, D.A.,Graham, D.E.,Kovalevsky, A.
L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study.
Structure, 22:1287-1300, 2014

PubMed Abstract: 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.

PubMed: 25132082
DOI: 10.1016/j.str.2014.07.002

Experimental method

X-RAY DIFFRACTION (1.7 Å)