4QE4

Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribulose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study.

Langan, P.Sangha, A.K.Wymore, T.Parks, J.M.Yang, Z.K.Hanson, B.L.Fisher, Z.Mason, S.A.Blakeley, M.P.Forsyth, V.T.Glusker, J.P.Carrell, H.L.Smith, J.C.Keen, D.A.Graham, D.E.Kovalevsky, A.

(2014) Structure 22: 1287-1300

  • DOI: 10.1016/j.str.2014.07.002
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimeri ...

    D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that the mechanism of ring-opening is the same as for the reaction with D-xylose. Structural evidence and QM/MM calculations show that in the reactive Michaelis complex L-arabinose is distorted to the high-energy (5)S1 conformation; this may explain the apparent high KM for this sugar. MD-FEP simulations indicate that amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose were found in furanose forms when bound to XI. We propose that these complexes containing Ni(2+) cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism.


    Organizational Affiliation

    Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. Electronic address: kovalevskyay@ornl.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
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
34V
Query on 34V

Download CCD File 
A
beta-L-ribulofuranose
C5 H10 O5
LQXVFWRQNMEDEE-YUPRTTJUSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.147 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.876α = 90
b = 99.63β = 90
c = 102.968γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
SHELXL-97refinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references