1O8B

Structure of Escherichia coli ribose-5-phosphate isomerase, RpiA, complexed with arabinose-5-phosphate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report



Literature

Structure of Escherichia Coli Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle

Zhang, R.-G.Andersson, C.E.Savchenko, A.Skarina, T.Evdokimova, E.Beasley, S.Arrowsmith, C.H.Edwards, A.M.Joachimiak, A.Mowbray, S.L.

(2003) Structure 11: 31

  • DOI: 10.1016/s0969-2126(02)00933-4
  • Primary Citation of Related Structures:  
    1KS2, 1O8B

  • PubMed Abstract: 
  • Ribose-5-phosphate isomerase A (RpiA; EC 5.3.1.6) interconverts ribose-5-phosphate and ribulose-5-phosphate. This enzyme plays essential roles in carbohydrate anabolism and catabolism; it is ubiquitous and highly conserved. The structure of RpiA from ...

    Ribose-5-phosphate isomerase A (RpiA; EC 5.3.1.6) interconverts ribose-5-phosphate and ribulose-5-phosphate. This enzyme plays essential roles in carbohydrate anabolism and catabolism; it is ubiquitous and highly conserved. The structure of RpiA from Escherichia coli was solved by multiwavelength anomalous diffraction (MAD) phasing, and refined to 1.5 A resolution (R factor 22.4%, R(free) 23.7%). RpiA exhibits an alpha/beta/(alpha/beta)/beta/alpha fold, some portions of which are similar to proteins of the alcohol dehydrogenase family. The two subunits of the dimer in the asymmetric unit have different conformations, representing the opening/closing of a cleft. Active site residues were identified in the cleft using sequence conservation, as well as the structure of a complex with the inhibitor arabinose-5-phosphate at 1.25 A resolution. A mechanism for acid-base catalysis is proposed.


    Related Citations: 
    • Escherichia Coli Rpia Gene Encoding Ribose Phosphate Isomerase A
      Hove-Jensen, B., Maigaard, M.
      (1993) J Bacteriol 175: 5628

    Organizational Affiliation

    Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSE 5-PHOSPHATE ISOMERASEAB219Escherichia coliMutation(s): 0 
EC: 5.3.1.6
Find proteins for P0A7Z0 (Escherichia coli (strain K12))
Explore P0A7Z0 
Go to UniProtKB:  P0A7Z0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ABF
Query on ABF

Download CCD File 
A, B
5-O-phosphono-beta-D-arabinofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-SQOUGZDYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ABFKi :  2100000   nM  PDBBind
ABFKi:  2100000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.049α = 90.23
b = 42.4β = 100.98
c = 60.195γ = 98.98
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2003-01-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary