1UJ6

Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with arabinose-5-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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This is version 1.3 of the entry. See complete history


Literature

Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi)

Hamada, K.Ago, H.Sugahara, M.Nodake, Y.Kuramitsu, S.Miyano, M.

(2003) J Biol Chem 278: 49183-49190

  • DOI: https://doi.org/10.1074/jbc.M309272200
  • Primary Citation of Related Structures:  
    1UJ4, 1UJ5, 1UJ6

  • PubMed Abstract: 

    Ribose-5-phosphate isomerase (Rpi) acts as a key enzyme in the oxidative and reductive pentose-phosphate pathways for the conversion of ribose-5-phosphate (R5P) to ribulose-5-phosphate and vice versa. We have determined the crystal structures of Rpi from Thermus thermophilus HB8 in complex with the open chain form of the substrate R5P and the open chain form of the C2 epimeric inhibitor arabinose-5-phosphate as well as the apo form at high resolution. The crystal structures of both complexes revealed that these ring-opened epimers are bound in the active site in a mirror symmetry binding mode. The O1 atoms are stabilized by an oxyanion hole composed of the backbone amide nitrogens in the conserved motif. In the structure of the Rpi.R5P complex, the conversion moiety O1-C1-C2-O2 in cis-configuration interacts with the carboxyl oxygens of Glu-108 in a water-excluded environment. Furthermore, the C2 hydroxyl group is presumed to be highly polarized by short hydrogen bonding with the side chain of Lys-99. R5P bound as the ring-opened reaction intermediate clarified the high stereoselectivity of the catalysis and is consistent with an aldose-ketose conversion by Rpi that proceeds via a cis-enediolate intermediate.


  • Organizational Affiliation

    Structural Biophysics Laboratory, Highthroughput Factory, Hyogo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ribose 5-phosphate isomerase227Thermus thermophilusMutation(s): 0 
EC: 5.3.1.6
UniProt
Find proteins for Q72J47 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72J47 
Go to UniProtKB:  Q72J47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72J47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
A5P PDBBind:  1UJ6 Ki: 8.90e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.349α = 90
b = 62.541β = 90
c = 131.254γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations