Literature summary for 6.3.2.36 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 .

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Thermococcus kodakarensis

Molecular Weight [Da]

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

Natural Substrates/ Products (Substrates)

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

Organism

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

Substrates and Products (Substrate)

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

Subunits

Subunits	Comment	Organism
homodimer	2 x 30000, about, sequence calculation	Thermococcus kodakarensis
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

Synonyms	Comment	Organism
phosphopantothenate synthetase	-	Thermococcus kodakarensis
Pps	-	Thermococcus kodakarensis
TK1686	-	Thermococcus kodakarensis

Cofactor

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

General Information

General Information	Comment	Organism
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
additional information	enzyme structure and substrate binding analysis, structure comparisons, structure-function analysis, overview	Thermococcus kodakarensis
physiological function	enzyme PPS catalyzes the ATP-dependent condensation of 4-phosphopantoate and beta-alanine generating 4'-phosphopantothenate	Thermococcus kodakarensis