BRENDA - Enzyme Database

Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis

Kishimoto, A.; Kita, A.; Ishibashi, T.; Tomita, H.; Yokooji, Y.; Imanaka, T.; Atomi, H.; Miki, K.; Proteins 82, 1924-1936 (2014)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Cloned (Commentary)
Organism
6.3.2.36
gene TK1686, DNA and amino acid sequence determination and analysis, sequence comparisons
Thermococcus kodakarensis
Crystallization (Commentary)
EC Number
Crystallization (Commentary)
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
Commentary
Organism
Structure
6.3.2.36
Mg2+
required
Thermococcus kodakarensis
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
6.3.2.36
60000
-
about, gel filtration
Thermococcus kodakarensis
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
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
Commentary
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
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
6.3.2.36
ATP + (R)-4-phosphopantoate + beta-alanine
-
746403
Thermococcus kodakarensis
AMP + diphosphate + (R)-4'-phosphopantothenate
-
-
-
?
6.3.2.36
ATP + (R)-4-phosphopantoate + beta-alanine
-
746403
Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1
AMP + diphosphate + (R)-4'-phosphopantothenate
-
-
-
?
6.3.2.36
additional information
substrate binding structures, overview
746403
Thermococcus kodakarensis
?
-
-
-
?
6.3.2.36
additional information
substrate binding structures, overview
746403
Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1
?
-
-
-
?
Subunits
EC Number
Subunits
Commentary
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
Commentary
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
Commentary
Organism
Structure
6.3.2.36
ATP
nuleotide binding structure analysis, modeling, overview
Thermococcus kodakarensis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
6.3.2.36
gene TK1686, DNA and amino acid sequence determination and analysis, sequence comparisons
Thermococcus kodakarensis
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
6.3.2.36
ATP
nuleotide binding structure analysis, modeling, overview
Thermococcus kodakarensis
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
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 (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
6.3.2.36
Mg2+
required
Thermococcus kodakarensis
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
6.3.2.36
60000
-
about, gel filtration
Thermococcus kodakarensis
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
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
-
-
?
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
6.3.2.36
ATP + (R)-4-phosphopantoate + beta-alanine
-
746403
Thermococcus kodakarensis
AMP + diphosphate + (R)-4'-phosphopantothenate
-
-
-
?
6.3.2.36
ATP + (R)-4-phosphopantoate + beta-alanine
-
746403
Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1
AMP + diphosphate + (R)-4'-phosphopantothenate
-
-
-
?
6.3.2.36
additional information
substrate binding structures, overview
746403
Thermococcus kodakarensis
?
-
-
-
?
6.3.2.36
additional information
substrate binding structures, overview
746403
Thermococcus kodakarensis ATCC BAA-918 / JCM 12380 / KOD1
?
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
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
General Information
EC Number
General Information
Commentary
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
General Information (protein specific)
EC Number
General Information
Commentary
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