Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.66 kDa 
• Atom Count: 3378 
• Modelled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

4QDP

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

• DOI: 10.2210/pdb4QDP/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2014-05-14 Released: 2014-09-03 
• Deposition Author(s): Kovalevsky, A.Y., Langan, P.

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Experimental Data Snapshot

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• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

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

• PubMed: 25132082 
• 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. 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.

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Organizational Affiliation: 

Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces rubiginosus	Mutation(s): 0  Gene Names: xylA EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARB (Subject of Investigation/LOI)	D [auth A]	beta-L-arabinopyranose C5 H10 O5 SRBFZHDQGSBBOR-KLVWXMOXSA-N
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Space Group: I 2 2 2

• 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 = 93.93	α = 90
b = 99.693	β = 90
c = 102.973	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
d*TREK	data scaling
HKL-3000	data reduction
RETREAT	data reduction
HKL-3000	data scaling
RETREAT	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-14 
• Released Date: 2014-09-03 
Deposition Author(s): Kovalevsky, A.Y., Langan, P.

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