3ENQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1007/s10059-009-0010-6
  • Primary Citation of Related Structures:  

  • 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 fo ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribose-5-phosphate isomerase A
A, B
235Vibrio vulnificus (strain YJ016)Mutation(s): 0 
Gene Names: rpiA
EC: 5.3.1.6
Find proteins for Q7MHL9 (Vibrio vulnificus (strain YJ016))
Go to UniProtKB:  Q7MHL9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 77.094α = 90.00
b = 77.094β = 90.00
c = 189.995γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance