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Literature summary extracted from

  • Kona, F.; Tao, P.; Martin, P.; Xu, X.; Gatti, D.L.
    Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis (2009), Biochemistry, 48, 3610-3630.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.5.1.55 in Escherichia coli with plasmid pet28a Aquifex aeolicus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.5.1.55 data reading at -173°C Aquifex aeolicus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.5.1.55 0.0000066
-
 phosphoenolpyruvate same enzyme preparation as before, substitution with 5 microM Cu2+, pH 5.0, 40°C Aquifex aeolicus
2.5.1.55 0.00004
-
 phosphoenolpyruvate independently prepared enzyme, substitution with 50 microM Cd2+, pH 5.0, 40°C Aquifex aeolicus
2.5.1.55 0.00014
-
 phosphoenolpyruvate same enzyme preparation as following, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00015
-
 phosphoenolpyruvate same enzyme preparation as following, substitution with 5 microM Cu2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00016
-
 phosphoenolpyruvate independently prepared enzyme, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00016
-
 phosphoenolpyruvate recombinant enzyme produced in Escherichia coli, native Zn2+ and Fe2+ not substituted, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00028
-
 phosphoenolpyruvate same enzyme preparation as following, substitution with 50 microM Zn2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.0005
-
 D-arabinose 5-phosphate same enzyme preparation as following, substitution with 50 microM Zn2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00123
-
 D-arabinose 5-phosphate recombinant enzyme produced in Escherichia coli, native Zn2+ and Fe2+ not substituted, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00156
-
 D-arabinose 5-phosphate same enzyme preparation as following, substitution with 5 microM Cu2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.002
-
 D-arabinose 5-phosphate same enzyme preparation as following, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.00227
-
 D-arabinose 5-phosphate independently prepared enzyme, substitution with 50 microM Cd2+, pH 5.0, 40°C Aquifex aeolicus
2.5.1.55 0.00318
-
 D-arabinose 5-phosphate independently prepared enzyme, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.01926
-
 D-arabinose 5-phosphate same enzyme preparation as before, substitution with 5 microM Cu2+, pH 5.0, 40°C Aquifex aeolicus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.5.1.55 Cd2+ second in enzyme activity, square pyramidal delocalized electronic structure computed with quantum mechanics/molecular mechanics geometry optimization Aquifex aeolicus
2.5.1.55 Cu2+ third in enzyme activity, octahedral or distorted tetrahedral delocalized electronic structure computed with quantum mechanics/molecular mechanics geometry optimization, product is bound in its linear conformation in the crystal structure of the enzyme with Cu2+, greenish color of enzyme, new absorption peak at 380 nm instead of 505 nm Aquifex aeolicus
2.5.1.55 Fe2+ unsubstituted enzyme with lowest enzyme activity Aquifex aeolicus
2.5.1.55 additional information the type of metal bound in the active site affects the behavior of the enzyme in vivo and the rate of product release in the crystal environment Aquifex aeolicus
2.5.1.55 Zn2+ highest enzyme activity, square pyramidal delocalized electronic structure computed with quantum mechanics/molecular mechanics geometry optimization Aquifex aeolicus

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 Aquifex aeolicus
-
 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.55 Aquifex aeolicus O66496
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.5.1.55 enzyme purification followed by incubation with 50 microM Cd2+, Zn2+, or Cu2+ in 20 mM Tris-HCl buffer, pH 7.5, to substitute the metal ions Fe2+ or Co2+ Aquifex aeolicus

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
-
 Aquifex aeolicus 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.5.1.55 3-deoxy-D-manno-octulosonate 8-phosphate synthase
-
 Aquifex aeolicus
2.5.1.55 Kdo8P synthase
-
 Aquifex aeolicus
2.5.1.55 KDO8PS
-
 Aquifex aeolicus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.5.1.55 0.31
-
 phosphoenolpyruvate recombinant enzyme produced in Escherichia coli, native Zn2+ and Fe2+ not substituted, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.34
-
 phosphoenolpyruvate enzyme preparation 1, substitution with 5 microM Cu2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.36
-
 phosphoenolpyruvate enzyme preparation 1, substitution with 5 microM Cu2+, pH 5.0, 40°C Aquifex aeolicus
2.5.1.55 0.41
-
 phosphoenolpyruvate enzyme preparation 1, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.46
-
 phosphoenolpyruvate independent enzyme preparation 2, substitution with 50 microM Cd2+, pH 5.0, 40°C Aquifex aeolicus
2.5.1.55 0.47
-
 phosphoenolpyruvate enzyme preparation 1, substitution with 50 microM Zn2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus
2.5.1.55 0.48
-
 phosphoenolpyruvate independent preparation 2 enzyme, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C Aquifex aeolicus

General Information

EC Number General Information Comment Organism
2.5.1.55 metabolism catalyzes the formation of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P), a key precursor in the biosynthesis of the endotoxin of Gram-negative bacteria Aquifex aeolicus