3CWH

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


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Observed: 0.237 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose

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.

(2008) Biochemistry 47: 7595-7597

  • DOI: https://doi.org/10.1021/bi8005434
  • Primary Citation of Related Structures:  
    3CWH

  • 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.


  • Organizational Affiliation

    M888, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase388Streptomyces rubiginosusMutation(s): 0 
EC: 5.3.1.5
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Observed: 0.237 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.64α = 90
b = 99.97β = 90
c = 103.97γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SHELXL-97refinement
d*TREKdata reduction
LAUENORMdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description