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:  
    4QDP, 4QDW, 4QE1, 4QE4, 4QE5, 4QEE, 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylose isomeraseA388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARB
Query on ARB
Download Ideal Coordinates CCD File 
D [auth A]beta-L-arabinopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KLVWXMOXSA-N		 Ligand Interaction
CD
Query on CD
Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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