1DIE

OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.151 

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This is version 1.3 of the entry. See complete history


Literature

Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase.

Collyer, C.A.Blow, D.M.

(1990) Proc Natl Acad Sci U S A 87: 1362-1366

  • DOI: 10.1073/pnas.87.4.1362
  • Primary Citation of Related Structures:  
    1DID, 1DIE

  • PubMed Abstract: 
  • Crystallographic studies of D-xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) incubated to equilibrium with substrate/product mixtures of xylose and xylulose show electron density for a bound intermediate. The accumulation of this bound intermediate shows that the mechanism is a non-Michaelis type ...

    Crystallographic studies of D-xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) incubated to equilibrium with substrate/product mixtures of xylose and xylulose show electron density for a bound intermediate. The accumulation of this bound intermediate shows that the mechanism is a non-Michaelis type. Carrell et al. [Carrell, H. L., Glusker, J. P., Burger, V., Manfre, F., Tritsch, D. & Biellmann, J.-F. (1989) Proc. Natl. Acad. Sci. USA 86, 4440-4444] and the present authors studied crystals of the enzyme-substrate complex under different conditions and made different interpretations of the substrate density, leading to different conclusions about the enzyme mechanism. All authors agree that the bound intermediate of the sugar is in an open-chain form. It is suggested that the higher-temperature study of Carrell et al. may have produced an equilibrium of multiple states, whose density fits poorly to the open-chain substrate, and led to incorrect interpretation. The two groups also bound different closed-ring sugar analogues to the enzyme, but these analogues bind differently. A possible explanation consistent with all the data is that the enzyme operates by a hydride shift mechanism.


    Related Citations: 
    • Mechanism for Aldose-Ketose Interconversion by D-Xylose Isomerase Involving Ring Opening Followed by a 1,2-Hydride Shift
      Collyer, C.A., Henrick, K., Blow, D.M.
      (1990) J Mol Biol 212: 211
    • Structures of D-Xylose Isomerase from Arthrobacter Strain B3728 Containing the Inhibitors Xylitol and D-Sorbitol at 2.5 Angstroms and 2.3 Angstroms Resolution, Respectively
      Henrick, K., Collyer, C.A., Blow, D.M.
      (1989) J Mol Biol 208: 129

    Organizational Affiliation

    Blackett Laboratory, Imperial College, London, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-XYLOSE ISOMERASEA, B394Arthrobacter sp. NRRL B3728Mutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P12070 (Arthrobacter sp. (strain NRRL B3728))
Explore P12070 
Go to UniProtKB:  P12070
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12070
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.151 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.6α = 90
b = 105.6β = 90
c = 153.4γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other