Literature summary for 2.5.1.55 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.

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

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

Inhibitors

Inhibitors	Comment	Organism
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
additional information	21 inhibitor compounds synthesis and screening based on the API inhibitor structure, docking study and molecular modelling, overview	Helicobacter pylori
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

Metals/Ions	Comment	Organism
Cd2+	activates, stabilizes, active site bound by Cys18, His204, Glu241, and Asp252	Helicobacter pylori
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
Zn2+	activates, stabilizes, active site bound	Helicobacter pylori

Molecular Weight [Da]

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

Natural Substrates/ Products (Substrates)

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

Organism

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

Purification (Commentary)

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

Substrates and Products (Substrate)

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

Subunits

Subunits	Comment	Organism
homodimer	2 * 30300, SDS-PAGE, two monomers in each asymmetric unit. The monomers adopt the (beta/alpha)8 barrel topology	Helicobacter pylori
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

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

Temperature Stability [°C]

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

General Information

General Information	Comment	Organism
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