1XLM

D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

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This is version 1.5 of the entry. See complete history


Literature

Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement.

Gerczei, T.Bocskei, Z.Szabo, E.Asboth, B.Naray-Szabo, G.

(1999) Int J Biol Macromol 25: 329-336

  • DOI: https://doi.org/10.1016/s0141-8130(99)00051-3
  • Primary Citation of Related Structures:  
    1XLM

  • PubMed Abstract: 

    The structure of the D254.256E double mutant of Arthrobacter xylose isomerase with Al3+ at both metal-binding sites was determined by the molecular replacement method at a conventional R-factor of 0.179. Binding of the two Al3+ does not alter the overall structure significantly. However, there are local rearrangements in the octahedral co-ordination sphere of the Al3+. The inhibitor molecule moves somewhat away from the active site. Furthermore, evidence was revealed for metal ion movement from site 2(1) to site 2(2) upon double mutation. Xylose isomerase requires two divalent metal cations for activation. The catalytic metal ion is translocated 1.8 A away from its initial position during the catalytic reaction. The fact that both activating and inactivating metals (including Al3+) were found exclusively at a single location in the double mutant was an indication that the consequently missing shuttle may account for the crippled catalytic efficiency.


  • Organizational Affiliation

    Department of Theoretical Chemistry, L. Eötvös University, Budapest, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-XYLOSE ISOMERASE
A, B
394Arthrobacter sp. NRRL B3728Mutation(s): 2 
EC: 5.3.1.5
UniProt
Find proteins for P12070 (Arthrobacter sp. (strain NRRL B3728))
Explore P12070 
Go to UniProtKB:  P12070
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12070
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.6α = 90
b = 140.7β = 90
c = 83.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
bioteXdata reduction
bioteXdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-04
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Other, Refinement description, Structure summary
  • Version 1.4: 2021-11-03
    Changes: Database references, Structure summary
  • Version 1.5: 2023-08-09
    Changes: Refinement description