4DVO

Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Go to UniProtKB:  P24300
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
SOR
Query on SOR

Download SDF File 
Download CCD File 
A
D-SORBITOL
C6 H14 O6
FBPFZTCFMRRESA-JGWLITMVSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
nCNSrefinement

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
  • Version 1.2: 2017-11-15
    Type: Refinement description