4DUO

Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.

Kovalevsky, A.Hanson, B.L.Mason, S.A.Forsyth, V.T.Fisher, Z.Mustyakimov, M.Blakeley, M.P.Keen, D.A.Langan, P.

(2012) Acta Crystallogr.,Sect.D 68: 1201-1206

  • DOI: 10.1107/S0907444912024808
  • Primary Citation of Related Structures:  4DVO

  • PubMed Abstract: 
  • D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of poly ...

    D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylose isomerase
A
388Streptomyces rubiginosusGene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Go to UniProtKB:  P24300
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYL
Query on XYL

Download SDF File 
Download CCD File 
A
D-XYLITOL
C5 H12 O5
HEBKCHPVOIAQTA-SCDXWVJYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.141 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.790α = 90.00
b = 99.620β = 90.00
c = 102.830γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
SCALAdata scaling
SHELXL-97refinement
PHASERphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-03
    Type: Database references