3CWH

D-xylose Isomerase in complex with linear product, per-deuterated xylulose

Summary for 3CWH

• Entry DOI: 10.2210/pdb3cwh/pdb
• Related: 2GVE
• Descriptor: Xylose isomerase, D-XYLULOSE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: enzyme-product complex, carbohydrate metabolism, isomerase, magnesium, metal-binding, pentose shunt, xylose metabolism
• Biological source: Streptomyces rubiginosus
• Cellular location: Cytoplasm: P24300
• Total number of polymer chains: 1
• Total formula weight: 43499.04

Authors

Kovalevsky, A.Y.,Langan, P.,Glusker, J.P. (deposition date: 2008-04-21, release date: 2008-08-05, Last modification date: 2023-08-30)

Primary citation

Kovalevsky, A.Y.,Katz, A.K.,Carrell, H.L.,Hanson, L.,Mustyakimov, M.,Fisher, S.Z.,Coates, L.,Schoenborn, B.P.,Bunick, G.J.,Glusker, J.P.,Langan, P.
Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose
Biochemistry, 47:7595-7597, 2008

PubMed Abstract: The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme d-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, d-xylulose, shows, unexpectedly, that O5 of d-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.

PubMed: 18578508
DOI: 10.1021/bi8005434

Experimental method

NEUTRON DIFFRACTION (2.2 Å)