Structure of PEP and zinc bound KDO8PS from H.pylori

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS).

Cho, S.Im, H.Lee, K.Y.Chen, J.Kang, H.J.Yoon, H.J.Min, K.H.Lee, K.R.Park, H.J.Lee, B.J.

(2016) Eur J Med Chem 108: 188-202

  • DOI: https://doi.org/10.1016/j.ejmech.2015.11.036
  • Primary Citation of Related Structures:  
    4Z1A, 4Z1B, 4Z1C, 4Z1D

  • PubMed Abstract: 

    The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDO8PS) from Helicobacter pylori (HpKDO8PS) was determined alone and within various complexes, revealing an extra helix (HE) that is absent in the structures of KDO8PS from other organisms. In contrast to the metal coordination of the KDO8PS enzyme from Aquifex aeolicus, HpKDO8PS is specifically coordinated with Cd(2+) or Zn(2+) ions, and isothermal titration calorimetry (ITC) and differential scanning fluorimetry (DSF) revealed that Cd(2+) thermally stabilizes the protein structure more efficiently than Zn(2+). In the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. Using the structures of HpKDO8PS and API [arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) bisubstrate inhibitor], we generated 21 compounds showing potential HpKDO8PS-binding properties via in silico virtual screening. The capacity of three, avicularin, hyperin, and MC181, to bind to HpKDO8PS was confirmed through saturation transfer difference (STD) experiments, and we identified their specific ligand binding modes by combining competition experiments and docking simulation analysis. Hyperin was confirmed to bind to the A5P binding site, primarily via hydrophilic interaction, whereas MC181 bound to both the PEP and A5P binding sites through hydrophilic and hydrophobic interactions. These results were consistent with the epitope mapping by STD. Our results are expected to provide clues for the development of HpKDO8PS inhibitors.

  • Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase
A, B
276Helicobacter pylori 26695Mutation(s): 0 
Gene Names: kdsAHP_0003
Find proteins for P56060 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56060 
Go to UniProtKB:  P56060
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56060
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.3α = 90
b = 51.013β = 104.37
c = 78.547γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references