Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-allose

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics.

Jung, J.Kim, J.K.Yeom, S.J.Ahn, Y.J.Oh, D.K.Kang, L.W.

(2011) Appl Microbiol Biotechnol 90: 517-527

  • DOI: https://doi.org/10.1007/s00253-011-3095-8
  • Primary Citation of Related Structures:  
    3HE8, 3HEE, 3PH3, 3PH4

  • PubMed Abstract: 

    Ribose-5-phosphate isomerase (Rpi) catalyzes the conversion of D-ribose 5-phosphate (R5P) to D-ribulose 5-phosphate, which is an important step in the non-oxidative pathway of the pentose phosphate pathway and the Calvin cycle of photosynthesis. Recently, Rpis have been used to produce valuable rare sugars for industrial purposes. Of the Rpis, D-ribose-5-phosphate isomerase B from Clostridium thermocellum (CtRpi) has the fastest reactions kinetics. While Thermotoga maritime Rpi (TmRpi) has the same substrate specificity as CtRpi, the overall activity of CtRpi is approximately 200-fold higher than that of TmRpi. To understand the structural basis of these kinetic differences, we determined the crystal structures, at 2.1-Å resolution or higher, of CtRpi alone and bound to its substrates, R5P, D-ribose, and D-allose. Structural comparisons of CtRpi and TmRpi showed overall conservation of their structures with two notable differences. First, the volume of the CtRpi substrate binding pocket (SBP) was 20% less than that of the TmRpi SBP. Second, the residues next to the sugar-ring opening catalytic residue (His98) were different. We switched the key residues, involved in SBP shaping or catalysis, between CtRpi and TmRpi by site-directed mutagenesis, and studied the enzyme kinetics of the mutants. We found that tight interactions between the two monomers, narrow SBP width, and the residues near the catalytic residue are all critical for the fast enzyme kinetics of CtRpi.

  • Organizational Affiliation

    Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-5-phosphate isomerase
A, B
169Acetivibrio thermocellus ATCC 27405Mutation(s): 0 
Gene Names: Cthe_2597
Find proteins for A3DIL8 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DIL8 
Go to UniProtKB:  A3DIL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DIL8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.134α = 90
b = 69.134β = 90
c = 154.284γ = 120
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: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description