4Z1A

Structure of apo form KDO8PS from H.pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.ejmech.2015.11.036
  • Primary Citation of Related Structures:  

  • 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 o ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-dehydro-3-deoxyphosphooctonate aldolase
A, B
276Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: kdsA
EC: 2.5.1.55
Find proteins for P56060 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56060
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 137.829α = 90.00
b = 50.657β = 110.51
c = 78.670γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2007-0056817
National Research Foundation of KoreaKorea, Republic Of2012R1A2A1A01003569
National Research Foundation of KoreaKorea, Republic Of2008-355-E00019
National Research Foundation of KoreaKorea, Republic Of2014R1A1A3A04050250
Ministry for Health, Welfare and Family Affairs, Republic of KoreaKorea, Republic OfA092006

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release