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)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.273 

  • Resolution: 1.53 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.199 

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This is version 1.5 of the entry. See complete history


Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.

Kovalevsky, A.Y.Hanson, L.Fisher, S.Z.Mustyakimov, M.Mason, S.A.Forsyth, V.T.Blakeley, M.P.Keen, D.A.Wagner, T.Carrell, H.L.Katz, A.K.Glusker, J.P.Langan, P.

(2010) Structure 18: 688-699

  • DOI: https://doi.org/10.1016/j.str.2010.03.011
  • Primary Citation of Related Structures:  
    3KBM, 3KBN, 3KBS, 3KBV, 3KBW, 3KCL, 3KCO

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545, USA. ayk@lanl.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.273 
  • Space Group: I 2 2 2
  • Resolution: 1.53 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.199 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.007α = 90
b = 99.669β = 90
c = 102.862γ = 90
Software Package:
Software NamePurpose
PCSdata collection
d*TREKdata reduction
LAUENORMdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Data collection
  • Version 1.3: 2018-04-25
    Changes: Data collection
  • Version 1.4: 2018-06-20
    Changes: Data collection
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary