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Literature summary extracted from

  • Kishimoto, A.; Kita, A.; Ishibashi, T.; Tomita, H.; Yokooji, Y.; Imanaka, T.; Atomi, H.; Miki, K.
    Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis (2014), Proteins, 82, 1924-1936 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.3.2.36 gene TK1686, DNA and amino acid sequence determination and analysis, sequence comparisons Thermococcus kodakarensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.3.2.36 purified free enzyme, and enzyme in complexes with ATP, and ATP and 4-phosphopantoate, sitting drop vapor diffusion method, for the free enzyme: mixing of 0.001 ml of 20 mg/ml of protein in 50 mM Tris-HC, pH 8.0, and 150 mM NaCl, with 0.001 ml of reservoir solution containing 18-20% PEG 3350, 200 mM ammonium acetate, and 100 mM Bis-Tris, pH 6.5, 20°C, 1 week, method optimization, for the enzyme-ATP-Mg2+ complex: 20 mg/ml protein is incubated for several hours at 4°C in the presence of 10 mM ATP and 10 mM MgCl2, mixing of 0.001 ml protein solution with 0.001 ml of reservoir solution containing 17% PEG 10000, 100 mM ammonium acetate, and 100 mM Bis-Tris, pH 5.5, equilibration with reservoir solution, 20°C, 2 weeks, for the enzyme-ATP-Mg2+-4-phosphopantoate complex, mixing of 0.001 ml of 20 mg/ml of protein in 50 mM Tris-HC, pH 8.0, 150 mM NaCl, mM ATP, 5 mM MgCl2, and 5 mM PPo, with 0.001 ml of reservoir solution containing 50% tacsimate, pH 4.0, 1% PEG 3350, and 100 mM sodium acetate trihydrate, pH 4.5, 4°C, 3 days, X-ray diffraction structure determination and analysis at 2.0-2.4 A resolution Thermococcus kodakarensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.3.2.36 Mg2+ required Thermococcus kodakarensis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
6.3.2.36 60000
-
 about, gel filtration Thermococcus kodakarensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6.3.2.36 ATP + (R)-4-phosphopantoate + beta-alanine Thermococcus kodakarensis
-
 AMP + diphosphate + (R)-4'-phosphopantothenate
-
 ?
6.3.2.36 ATP + (R)-4-phosphopantoate + beta-alanine Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1
-
 AMP + diphosphate + (R)-4'-phosphopantothenate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
6.3.2.36 Thermococcus kodakarensis Q5JIZ8
-
-
6.3.2.36 Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1 Q5JIZ8
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.3.2.36 ATP + (R)-4-phosphopantoate + beta-alanine
-
 Thermococcus kodakarensis AMP + diphosphate + (R)-4'-phosphopantothenate
-
 ?
6.3.2.36 ATP + (R)-4-phosphopantoate + beta-alanine
-
 Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1 AMP + diphosphate + (R)-4'-phosphopantothenate
-
 ?
6.3.2.36 additional information substrate binding structures, overview Thermococcus kodakarensis ?
-
 ?
6.3.2.36 additional information substrate binding structures, overview Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
6.3.2.36 homodimer 2 x 30000, about, sequence calculation Thermococcus kodakarensis
6.3.2.36 More PPS forms an asymmetric homodimer, in which two monomers composing a dimer, deviated from the exact twofold symmetry, displaying 4°–13° distortion Thermococcus kodakarensis

Synonyms

EC Number Synonyms Comment Organism
6.3.2.36 phosphopantothenate synthetase
-
 Thermococcus kodakarensis
6.3.2.36 Pps
-
 Thermococcus kodakarensis
6.3.2.36 TK1686
-
 Thermococcus kodakarensis

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.36 ATP nuleotide binding structure analysis, modeling, overview Thermococcus kodakarensis

General Information

EC Number General Information Comment Organism
6.3.2.36 metabolism the common pathway for coenzyme A biosynthesis which involves two enzymes to convert pantoate to 4'-phosphopantothenate involves two enzymes, pantoate kinase, and phosphopantothenate synthetase (PPS), they are responsible for this conversion in archaea. In archea, In these archaea, pantoate is phosphorylated by PoK to produce 4-phosphopantoate (PPo), and then condensation of PPo and beta-alanine is catalyzed by PPS, generating 4'-phosphopantothenate Thermococcus kodakarensis
6.3.2.36 additional information enzyme structure and substrate binding analysis, structure comparisons, structure-function analysis, overview Thermococcus kodakarensis
6.3.2.36 physiological function enzyme PPS catalyzes the ATP-dependent condensation of 4-phosphopantoate and beta-alanine generating 4'-phosphopantothenate Thermococcus kodakarensis