Substrate and inhibitor complexes of ribose 5-phosphate isomerase from Vibrio vulnificus YJ016

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

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Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016

Kim, T.G.Kwon, T.H.Min, K.Dong, M.S.Park, Y.I.Ban, C.

(2009) Mol Cells 27: 99-103

  • DOI: https://doi.org/10.1007/s10059-009-0010-6
  • Primary Citation of Related Structures:  
    3ENQ, 3ENV, 3ENW

  • PubMed Abstract: 

    Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at 2.0 A resolution. VvRpiA is highly similar to Eschericihia coliRpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.

  • Organizational Affiliation

    Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-5-phosphate isomerase A
A, B
235Vibrio vulnificusMutation(s): 0 
Gene Names: rpiA
Find proteins for Q7MHL9 (Vibrio vulnificus (strain YJ016))
Explore Q7MHL9 
Go to UniProtKB:  Q7MHL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MHL9
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.062α = 90
b = 77.062β = 90
c = 189.258γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    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