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3kco

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3kco, resolution 1.80Å ()
Sites: , , and
Ligands: , ,
Gene: xylA (Streptomyces rubiginosus)
Activity: Xylose isomerase, with EC number 5.3.1.5
Related: 3kbj, 3kbm, 3kbn, 3kbs, 3kbv, 3kbw, 3kcj, 3kcl


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Room temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN)

Publication Abstract from PubMed

Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study., Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P, Structure. 2010 Jun 9;18(6):688-99. PMID:20541506

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3kco is a 1 chain structure with sequence from Streptomyces rubiginosus. Full crystallographic information is available from OCA.

Reference

  • Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P. Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study. Structure. 2010 Jun 9;18(6):688-99. PMID:20541506 doi:10.1016/j.str.2010.03.011

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