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Literature summary extracted from

  • 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.
    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) (2016), Eur. J. Med. Chem., 108, 188-202.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.5.1.55 gene kdsA, recombinant expression of His-tagged enzyme in Escherichia coli strain pTf16/BL21 Helicobacter pylori

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.5.1.55 purified recombinant His-tagged wild-type and mutant H204A enzymes in apoform, or wild-type enzyme complexed with Zn2+ or Cd2+, hanging drop vapor diffusion method, mixing of 0.001 ml of protein solution, containing inhibitor in a 1:2 ratio, with 0.001 ml of reservoir solution, containing 18% PEG 3350, 0.1 M HEPES, pH 7.5, and 0.25 M magnesium chloride hexahydrate, equilibration against reservoir solution, 20°C, 14 days, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement and modelling Helicobacter pylori

Protein Variants

EC Number Protein Variants Comment Organism
2.5.1.55 H204A site-directed mutagenesis, crystal structure analysis Helicobacter pylori

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.5.1.55 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-[[(1R,2R,3S,4S,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]oxy]-4H-chromen-4-one i.e. hyperin, structure analysis, and enzyme interaction study, binding structure, overview Helicobacter pylori
2.5.1.55 additional information 21 inhibitor compounds synthesis and screening based on the API inhibitor structure, docking study and molecular modelling, overview Helicobacter pylori
2.5.1.55 N-[3-(furan-2-yl)phenyl]-1-(3-phenylpropyl)piperidine-4-carboxamide i.e. MC181, structure analysis, and enzyme interaction study, binding structure, overview Helicobacter pylori

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.5.1.55 Cd2+ activates, stabilizes, active site bound by Cys18, His204, Glu241, and Asp252 Helicobacter pylori
2.5.1.55 additional information the enzyme is specifically coordinated with Cd2+ or Zn2+ ions, and isothermal titration calorimetry and differential scanning fluorimetry reveal that Cd2+ thermally stabilizes the protein structure more efficiently than Zn2 Helicobacter pylori
2.5.1.55 Zn2+ activates, stabilizes, active site bound Helicobacter pylori

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
2.5.1.55 30300
-
-
 Helicobacter pylori

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.5.1.55 phosphoenolpyruvate + D-arabinose 5-phosphate + H2O Helicobacter pylori
-
 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.55 Helicobacter pylori P56060 gene HP_0003 or kdsA
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.5.1.55 recombinant His-tagged enzyme in Escherichia coli strain pTf16/BL21 by nickel affinity chromatography, dialysis, and ultrafiltration Helicobacter pylori

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.5.1.55 phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
-
 Helicobacter pylori 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.5.1.55 homodimer 2 * 30300, SDS-PAGE, two monomers in each asymmetric unit. The monomers adopt the (beta/alpha)8 barrel topology Helicobacter pylori
2.5.1.55 More in the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure Helicobacter pylori

Synonyms

EC Number Synonyms Comment Organism
2.5.1.55 3-deoxy-D-manno-octulosonate-8-phosphate synthase
-
 Helicobacter pylori
2.5.1.55 HpKDO8PS
-
 Helicobacter pylori
2.5.1.55 KDO8PS
-
 Helicobacter pylori

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
2.5.1.55 additional information
-
 Cd2+ thermally stabilizes the protein structure more efficiently than Zn2+ Helicobacter pylori

General Information

EC Number General Information Comment Organism
2.5.1.55 additional information in the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. The active site is formed by residues the active site Lys52, Asn54, Arg55, Gln133, Asp252, and Asn255 Helicobacter pylori