1DID

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


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.USA 87: 1362-1366

  • Primary Citation of Related Structures:  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 inter ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-XYLOSE ISOMERASE
A, B
394Arthrobacter sp. (strain NRRL B3728)Gene Names: xylA
EC: 5.3.1.5
Find proteins for P12070 (Arthrobacter sp. (strain NRRL B3728))
Go to UniProtKB:  P12070
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DIG
Query on DIG

Download SDF File 
Download CCD File 
A, B
2,5-DIDEOXY-2,5-IMINO-D-GLUCITOL
C6 H13 N O4
PFYHYHZGDNWFIF-JGWLITMVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.100α = 90.00
b = 106.100β = 90.00
c = 153.300γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other