Structure of L-ribulose 3-epimerase

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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This is version 1.2 of the entry. See complete history


Structural insight into L-ribulose 3-epimerase from Mesorhizobium loti.

Uechi, K.Sakuraba, H.Yoshihara, A.Morimoto, K.Takata, G.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2330-2339

  • DOI: https://doi.org/10.1107/S0907444913021665
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    L-Ribulose 3-epimerase (L-RE) from Mesorhizobium loti has been identified as the first ketose 3-epimerase that shows the highest observed activity towards ketopentoses. In the present study, the crystal structure of the enzyme was determined to 2.7 Å resolution. The asymmetric unit contained two homotetramers with the monomer folded into an (α/β)8-barrel carrying four additional short α-helices. The overall structure of M. loti L-RE showed significant similarity to the structures of ketose 3-epimerases from Pseudomonas cichorii, Agrobacterium tumefaciens and Clostridium cellulolyticum, which use ketohexoses as preferred substrates. However, the size of the C-terminal helix (α8) was much larger in M. loti L-RE than the corresponding helices in the other enzymes. In M. loti L-RE the α8 helix and the following C-terminal tail possessed a unique subunit-subunit interface which promoted the formation of additional intermolecular interactions and strengthened the enzyme stability. Structural comparisons revealed that the relatively small hydrophobic pocket of the enzyme around the substrate was likely to be the main factor responsible for the marked specificity for ketopentoses shown by M. loti L-RE.

  • Organizational Affiliation

    Rare Sugar Research Center, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-ribulose 3-epimerase
A, B, C, D, E
A, B, C, D, E, F, G, H
297Mesorhizobium lotiMutation(s): 0 
EC: 5.3.1
Find proteins for N0DP12 (Rhizobium loti)
Explore N0DP12 
Go to UniProtKB:  N0DP12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN0DP12
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
O [auth D],
Q [auth E]
C6 H14 O2
Query on MN

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
N [auth D]
P [auth E]
I [auth A],
K [auth B],
M [auth C],
N [auth D],
P [auth E],
R [auth F],
S [auth G],
T [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.511α = 90
b = 206.234β = 90
c = 121.975γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description