1K0W

CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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This is version 1.3 of the entry. See complete history. 


Literature

The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization

Luo, Y., Samuel, J., Mosimann, S.C., Lee, J.E., Tanner, M.E., Strynadka, N.C.J.

(2001) Biochemistry 40: 14763-14771

  • DOI: 10.1021/bi0112513
  • Primary Citation of Related Structures:  
    1JDI, 1K0W

  • PubMed Abstract: 

    • The structure of L-ribulose-5-phosphate 4-epimerase from E. coli has been solved to 2.4 A resolution using X-ray diffraction data. The structure is homo-tetrameric and displays C(4) symmetry. Each subunit has a single domain comprised of a central beta-sheet flanked on either side by layers of alpha-helices ...

    The structure of L-ribulose-5-phosphate 4-epimerase from E. coli has been solved to 2.4 A resolution using X-ray diffraction data. The structure is homo-tetrameric and displays C(4) symmetry. Each subunit has a single domain comprised of a central beta-sheet flanked on either side by layers of alpha-helices. The active site is identified by the position of the catalytic zinc residue and is located at the interface between two adjacent subunits. A remarkable feature of the structure is that it shows a very close resemblance to that of L-fuculose-1-phosphate aldolase. This is consistent with the notion that both enzymes belong to a superfamily of epimerases/aldolases that catalyze carbon-carbon bond cleavage reactions via a metal-stabilized enolate intermediate. Detailed inspection of the epimerase structure, however, indicates that despite the close overall structural similarity to class II aldolases, the enzyme has evolved distinct active site features that promote its particular chemistry.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
A, B, C, D, E, F
A, B, C, D, E, F
231Escherichia coliMutation(s): 1 
Gene Names: araD
EC: 5.1.3.4
UniProt
Find proteins for P08203 (Escherichia coli (strain K12))
Explore P08203 
Go to UniProtKB:  P08203
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08203
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.9α = 90
b = 105.9β = 90
c = 274.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations