4QDP

Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Cd2+ ions and cyclic beta-L-arabinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  

  • 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

    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.,Chemistry Department, University of Toledo, Toledo, OH 43606, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. Electronic address: kovalevskyay@ornl.gov.,Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.,Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France; EPSAM/ISTM, Keele University, Staffordshire ST5 5BG, UK.,ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, Oxon, England.




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
ARB
Query on ARB

Download SDF File 
Download CCD File 
A
BETA-L-ARABINOSE
C5 H10 O5
SRBFZHDQGSBBOR-KLVWXMOXSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-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: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.231 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.930α = 90.00
b = 99.693β = 90.00
c = 102.973γ = 90.00
Software Package:
Software NamePurpose
RETREATdata scaling
CNSphasing
d*TREKdata scaling
nCNSrefinement
RETREATdata reduction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2018-04-25
    Type: Data collection
  • Version 1.4: 2018-06-20
    Type: Data collection