PDBsum entry 4z1b

Transferase

PDB id: 4z1b

Contents

Protein chains

256 a.a.

Waters ×180

PDB id:

4z1b

Name:

Transferase

Title:

Structure of h204a mutant kdo8ps from h.Pylori

Structure:

2-dehydro-3-deoxyphosphooctonate aldolase. Chain: a, b. Synonym: 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase,kdo-8- phosphate synthase,kdops,phospho-2-dehydro-3-deoxyoctonate aldolase. Engineered: yes. Mutation: yes

Source:

Helicobacter pylori (strain atcc 700392 / 26695). Organism_taxid: 85962. Strain: atcc 700392 / 26695. Gene: kdsa, hp_0003. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.186 R-free: 0.238

Authors:

B.J.Lee,S.Cho,H.Im,H.J.Yoon

Key ref:

S.Cho et al. (2016). 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). Eur J Med Chem, 108, 188-202. PubMed id: 26649906 DOI: 10.1016/j.ejmech.2015.11.036

Date:

27-Mar-15 Release date: 09-Mar-16

Protein chains

P56060  (KDSA_HELPY) -  2-dehydro-3-deoxyphosphooctonate aldolase from Helicobacter pylori (strain ATCC 700392 / 26695)

Seq: 276 a.a.

Struc: 256 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase.
• Reaction: D-arabinose 5-phosphate + phosphoenolpyruvate + H2O = 3-deoxy-alpha-D- manno-2-octulosonate-8-phosphate + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.ejmech.2015.11.036

Eur J Med Chem 108:188-202 (2016)

PubMed id: 26649906

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).

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

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.