Crystal Structure Of apo-Kdo8P Synthase

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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Crystal Structures of Escherichia coli KDO8P Synthase Complexes Reveal the Source of Catalytic Irreversibility

Vainer, R.Belakhov, V.Rabkin, E.Baasov, T.Adir, N.

(2005) J Mol Biol 351: 641-652

  • DOI: https://doi.org/10.1016/j.jmb.2005.06.021
  • Primary Citation of Related Structures:  
    1PHW, 1Q3N, 1X6U, 1X8F

  • PubMed Abstract: 

    The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial modes of ligand binding in KDO8PS binary complexes by X-ray crystallography. Structures of the apo-enzyme and of binary complexes with the substrate PEP, the product KDO8P and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate (1dA5P) were obtained. The KDO8PS active site resembles an irregular funnel with positive electrostatic potential situated at the bottom of the PEP-binding sub-site, which is the primary attractive force towards negatively charged phosphate moieties of all ligands. The structures of the ligand-free apo-KDO8PS and the binary complex with the product KDO8P visualize for the first time the role of His202 as an active-site gate. Examination of the crystal structures of KDO8PS with the KDO8P or 1dA5P shows these ligands bound to the enzyme in the PEP-binding sub-site, and not as expected to the A5P sub-site. Taken together, the structures presented here strengthen earlier evidence that this enzyme functions predominantly through positional catalysis, map out the roles of active-site residues and provide evidence that explains the total lack of catalytic reversibility.

  • Organizational Affiliation

    Department of Chemistry and Institute of Catalysis, Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase284Escherichia coliMutation(s): 0 
Gene Names: kdsA
Find proteins for P0A715 (Escherichia coli (strain K12))
Explore P0A715 
Go to UniProtKB:  P0A715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A715
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.681α = 90
b = 118.681β = 90
c = 118.681γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Refinement description