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: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.5 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:  
    4QEE, 4QDW, 4QDP, 4QE1, 4QE4, 4QE5, 4QEH

  • 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 epimerization of L-arabinose to L-ribulose and L-ribose, respectively ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylose isomeraseA388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARB
Query on ARB

Download CCD File 
A
beta-L-arabinopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KLVWXMOXSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.93α = 90
b = 99.693β = 90
c = 102.973γ = 90
Software Package:
Software NamePurpose
nCNSrefinement
d*TREKdata scaling
HKL-3000data reduction
RETREATdata reduction
HKL-3000data scaling
RETREATdata scaling
CNSphasing

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
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-04-25
    Changes: Data collection
  • Version 1.4: 2018-06-20
    Changes: Data collection
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary