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Literature summary extracted from

  • Allison, T.M.; Cochrane, F.C.; Jameson, G.B.; Parker, E.J.
    Examining the role of intersubunit contacts in catalysis by 3-deoxy-D-manno-octulosonate 8-phosphate synthase (2013), Biochemistry, 52, 4676-4686.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.5.1.55 purified recombinant mutant enzymes, hanging-drop vapor diffusion, mixing of 0.002 ml of protein solution containing 20 mg/ml protein in 10 mM BTP, pH 7.5, with 0.002 ml of reservoir solution containing 100 mM sodium acetate, pH 4.6, and 0.6-3.0 M NaCl, equilibration against 0.5 ml reservoir solution, 20°C, 24 h, X-ray diffraction structure determination and analysis at 1.75-2.10 A resolution Neisseria meningitidis

Protein Variants

EC Number Protein Variants Comment Organism
2.5.1.55 F114A site-directed mutagenesis, conversion to the corresponding residue in enzyme DAH7PS, EC 2.5.1.54, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 F114R site-directed mutagenesis, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 F114R/R117A site-directed mutagenesis, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 F114R/R117Q site-directed mutagenesis, conversion to the corresponding residue in enzyme DAH7PS, EC 2.5.1.54, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 F114R/R117Q/F139G site-directed mutagenesis, conversion to the corresponding residue in enzyme DAH7PS, EC 2.5.1.54, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 F139G site-directed mutagenesis, conversion to the corresponding residue in enzyme DAH7PS, EC 2.5.1.54, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 R117K site-directed mutagenesis, conversion to the corresponding residue in enzyme DAH7PS, EC 2.5.1.54, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis
2.5.1.55 R117Q site-directed mutagenesis, conversion to the corresponding residue in enzyme DAH7PS, EC 2.5.1.54, the mutant shows altered kinetics compared to the wild-type, structure analysis Neisseria meningitidis

General Stability

EC Number General Stability Organism
2.5.1.55 Cd2+ destabilizes the enzyme, overview Neisseria meningitidis
2.5.1.55 substrate phosphoenolpyruvate stabilizes the wild-type and mutant enzymes Neisseria meningitidis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.5.1.55 additional information
-
additional information Michaelis-Menten kinetics Neisseria meningitidis
2.5.1.55 0.0025
-
phosphoenolpyruvate pH and temperature not specified in the publication Neisseria meningitidis
2.5.1.55 0.012
-
D-arabinose 5-phosphate pH and temperature not specified in the publication Neisseria meningitidis
2.5.1.55 0.014
-
phosphoenolpyruvate pH and temperature not specified in the publication, mutant F139A Neisseria meningitidis
2.5.1.55 0.022
-
phosphoenolpyruvate pH and temperature not specified in the publication, R117K Neisseria meningitidis
2.5.1.55 0.058
-
phosphoenolpyruvate pH and temperature not specified in the publication, mutant F114A Neisseria meningitidis
2.5.1.55 0.095
-
phosphoenolpyruvate pH and temperature not specified in the publication, mutant F114R Neisseria meningitidis
2.5.1.55 0.285
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R Neisseria meningitidis
2.5.1.55 0.594
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F139A Neisseria meningitidis
2.5.1.55 0.816
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, R117K Neisseria meningitidis
2.5.1.55 0.873
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114A Neisseria meningitidis
2.5.1.55 2.742
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R/R117Q Neisseria meningitidis
2.5.1.55 3.21
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, R117Q Neisseria meningitidis
2.5.1.55 3.6
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, F114R/R117Q/F139G Neisseria meningitidis
2.5.1.55 3.7
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R/R117A Neisseria meningitidis

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.5.1.55 Cd2+ destabilizes the enzyme, overview Neisseria meningitidis
2.5.1.55 additional information metal-independent enzyme. Mn2+ or Co2+ have no effect on enzyme stability Neisseria meningitidis

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 Neisseria meningitidis
-
3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
-
?

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.55 Neisseria meningitidis
-
-
-

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
-
Neisseria meningitidis 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
-
?

Subunits

EC Number Subunits Comment Organism
2.5.1.55 tetramer the enzyme adopts a homotetrameric associations with its active site close to one of the interfaces. The conserved PAFLxR motif in KDO8PS on the short beta4alpha4 loop of the (beta/alpha)8 barrel, form part of this interface and provide key contacts with substrates Neisseria meningitidis

Synonyms

EC Number Synonyms Comment Organism
2.5.1.55 3-deoxy-D-manno-octulosonate 8-phosphate synthase
-
Neisseria meningitidis
2.5.1.55 KDO8PS
-
Neisseria meningitidis
2.5.1.55 NmeKDO8PS
-
Neisseria meningitidis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.5.1.55 0.01
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, R117A Neisseria meningitidis
2.5.1.55 0.108
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R/R117A Neisseria meningitidis
2.5.1.55 0.14
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, F114R/R117Q/F139G Neisseria meningitidis
2.5.1.55 0.27
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R/R117Q Neisseria meningitidis
2.5.1.55 1.06
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, R117Q Neisseria meningitidis
2.5.1.55 3
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R Neisseria meningitidis
2.5.1.55 4.8
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, R117K Neisseria meningitidis
2.5.1.55 6.1
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114A Neisseria meningitidis
2.5.1.55 8
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, wild/type enzyme Neisseria meningitidis
2.5.1.55 8.6
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F139A Neisseria meningitidis

General Information

EC Number General Information Comment Organism
2.5.1.55 evolution KDO8PS is evolutionarily and structurally related to the first enzyme of the shikimate pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS, EC 2.5.1.54), which uses erythrose 4-phosphate in place of arabinose 5-phosphate. Both KDO8PS and type Ibeta DAH7PS enzymes adopt similar homotetrameric associations with their active sites close to one of the interfaces Neisseria meningitidis
2.5.1.55 physiological function the enzyme catalyzes the reaction between phosphoenolpyruvate and arabinose 5-phosphate in the first committed step in the pathway to 3-deoxy-D-manno-octulosonate, a component in the cell wall of Gram-negative bacteria Neisseria meningitidis

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.5.1.55 0.029
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R Neisseria meningitidis
2.5.1.55 0.039
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R/R117Q Neisseria meningitidis
2.5.1.55 0.1
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114R/R117A Neisseria meningitidis
2.5.1.55 0.33
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, R117Q Neisseria meningitidis
2.5.1.55 5.9
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, F114R/R117Q/F139G Neisseria meningitidis
2.5.1.55 7
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F139A Neisseria meningitidis
2.5.1.55 11
-
D-arabinose 5-phosphate pH and temperature not specified in the publication, mutant F114A Neisseria meningitidis
2.5.1.55 14
-
D-arabinose 5-phosphate pH and temperature not specified in the publication Neisseria meningitidis
2.5.1.55 660
-
D-arabinose 5-phosphate pH and temperature not specified in the publication Neisseria meningitidis