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Literature summary for 2.5.1.55 extracted from
- Examining the role of intersubunit contacts in catalysis by 3-deoxy-D-manno-octulosonate 8-phosphate synthase (2013), Biochemistry, 52, 4676-4686.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| 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
| Protein Variants | Comment | Organism |
|---|---|---|
| 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 |
| F114R | site-directed mutagenesis, the mutant shows altered kinetics compared to the wild-type, structure analysis | Neisseria meningitidis |
| F114R/R117A | site-directed mutagenesis, the mutant shows altered kinetics compared to the wild-type, structure analysis | Neisseria meningitidis |
| 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 |
| 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 |
| 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 |
| 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 |
| 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
| General Stability | Organism |
|---|---|
| Cd2+ destabilizes the enzyme, overview | Neisseria meningitidis |
| substrate phosphoenolpyruvate stabilizes the wild-type and mutant enzymes | Neisseria meningitidis |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Neisseria meningitidis | |
| 0.0025 | - |
phosphoenolpyruvate | pH and temperature not specified in the publication | Neisseria meningitidis |  |
| 0.012 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication | Neisseria meningitidis | |
| 0.014 | - |
phosphoenolpyruvate | pH and temperature not specified in the publication, mutant F139A | Neisseria meningitidis | |
| 0.022 | - |
phosphoenolpyruvate | pH and temperature not specified in the publication, R117K | Neisseria meningitidis | |
| 0.058 | - |
phosphoenolpyruvate | pH and temperature not specified in the publication, mutant F114A | Neisseria meningitidis | |
| 0.095 | - |
phosphoenolpyruvate | pH and temperature not specified in the publication, mutant F114R | Neisseria meningitidis | |
| 0.285 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R | Neisseria meningitidis | |
| 0.594 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F139A | Neisseria meningitidis | |
| 0.816 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, R117K | Neisseria meningitidis | |
| 0.873 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114A | Neisseria meningitidis | |
| 2.742 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R/R117Q | Neisseria meningitidis | |
| 3.21 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, R117Q | Neisseria meningitidis | |
| 3.6 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, F114R/R117Q/F139G | Neisseria meningitidis | |
| 3.7 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R/R117A | Neisseria meningitidis | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Cd2+ | destabilizes the enzyme, overview | Neisseria meningitidis | |
| additional information | metal-independent enzyme. Mn2+ or Co2+ have no effect on enzyme stability | Neisseria meningitidis |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| phosphoenolpyruvate + D-arabinose 5-phosphate + H2O | Neisseria meningitidis | - |
3-deoxy-D-manno-octulosonate 8-phosphate + phosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Neisseria meningitidis | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| phosphoenolpyruvate + D-arabinose 5-phosphate + H2O | - |
Neisseria meningitidis | 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| 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
| Synonyms | Comment | Organism |
|---|---|---|
| 3-deoxy-D-manno-octulosonate 8-phosphate synthase | - |
Neisseria meningitidis |
| KDO8PS | - |
Neisseria meningitidis |
| NmeKDO8PS | - |
Neisseria meningitidis |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.01 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, R117A | Neisseria meningitidis | |
| 0.108 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R/R117A | Neisseria meningitidis | |
| 0.14 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, F114R/R117Q/F139G | Neisseria meningitidis | |
| 0.27 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R/R117Q | Neisseria meningitidis | |
| 1.06 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, R117Q | Neisseria meningitidis | |
| 3 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R | Neisseria meningitidis | |
| 4.8 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, R117K | Neisseria meningitidis | |
| 6.1 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114A | Neisseria meningitidis | |
| 8 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, wild/type enzyme | Neisseria meningitidis | |
| 8.6 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F139A | Neisseria meningitidis | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| 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 |
| 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]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.029 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R | Neisseria meningitidis | |
| 0.039 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R/R117Q | Neisseria meningitidis | |
| 0.1 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114R/R117A | Neisseria meningitidis | |
| 0.33 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, R117Q | Neisseria meningitidis | |
| 5.9 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, F114R/R117Q/F139G | Neisseria meningitidis | |
| 7 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F139A | Neisseria meningitidis | |
| 11 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication, mutant F114A | Neisseria meningitidis | |
| 14 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication | Neisseria meningitidis | |
| 660 | - |
D-arabinose 5-phosphate | pH and temperature not specified in the publication | Neisseria meningitidis | |
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