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Literature summary for 2.7.9.1 extracted from

  • Lin, Y.; Lusin, J.D.; Ye, D.; Dunaway-Mariano, D.; Ames, J.B.
    Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase (2006), Biochemistry, 45, 1702-1711.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli [Clostridium] symbiosum

Crystallization (Commentary)

Crystallization (Comment) Organism
X-ray crystal structure mentioned, the central domain faces the C-terminal domain and positions the phosphorylated His residue for phosphoryl transfer to pyruvate thereby forming phosphoenolpyruvate and regenerating the unphosphorylated H455, native structure determined by NMR [Clostridium] symbiosum

General Stability

General Stability Organism
central domain protein Cent-I, 4.3 kcal/mol (delta G) for unfolding at 25°C in buffer at pH 7.0 [Clostridium] symbiosum

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ binds together with phosphate and ATP to the active site located at the concave surface of the N-terminal domain [Clostridium] symbiosum

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
additional information
-
mass spectral determination of Cent-I recombinant protein (residues 381-512 of the native PPDK), native molecular weight determined by gel filtration chromatography is 13438 [Clostridium] symbiosum
13438
-
1 * 13438, recombinant protein of the central domain of PPDK (Cent-I protein), mass spectrometry, chromatography [Clostridium] symbiosum
96000
-
x * 96000, PPDK of Clostridium symbiosum, three consecutive structural domains connected by helical linkers, X-ray crystal structure [Clostridium] symbiosum

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information [Clostridium] symbiosum central domain transports phosphoryl-groups between two distant catalytic sites located on the N-terminal and C-terminal sites, description of ability to catalyze the ATP/phosphate partial reaction by central domain and N-terminal domain of PPDK as independent recombinant proteins ?
-
?

Organism

Organism UniProt Comment Textmining
[Clostridium] symbiosum P22983
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant proteins of the central domain (Cent-I) and of the N-terminus (Tem-340, residues 1-340 of the native PPDK) [Clostridium] symbiosum

Renatured (Commentary)

Renatured (Comment) Organism
percent decrease of fluorescence intensity (304 nm) for conversion of native protein (0 M urea) to fully denaturation (6 M urea) calculated (23.5%), DELTA G for unfolding of Cent-I (PPDK central domain construct of residues 381-512) in solvent determined (4.3 kcal/mol) [Clostridium] symbiosum

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + PPDK central domain construct of residues 381-512 (Cent-I) + phosphate
-
[Clostridium] symbiosum ?
-
?
ATP + PPDK N-terminal domain construct of residues 1-340 (Tem-340) + phosphate
-
[Clostridium] symbiosum ?
-
?
ATP + PPDK N-terminal domain construct of residues 1-553 (Tem340-Cent-I) + phosphate
-
[Clostridium] symbiosum ?
-
?
ATP + pyruvate + phosphate
-
[Clostridium] symbiosum AMP + phosphoenolpyruvate + diphosphate
-
r
additional information central domain transports phosphoryl-groups between two distant catalytic sites located on the N-terminal and C-terminal sites, description of ability to catalyze the ATP/phosphate partial reaction by central domain and N-terminal domain of PPDK as independent recombinant proteins [Clostridium] symbiosum ?
-
?

Subunits

Subunits Comment Organism
homodimer x * 96000, PPDK of Clostridium symbiosum, three consecutive structural domains connected by helical linkers, X-ray crystal structure [Clostridium] symbiosum
monomer 1 * 13438, recombinant protein of the central domain of PPDK (Cent-I protein), mass spectrometry, chromatography [Clostridium] symbiosum
More multilayered structure of Cent-I protein in solution, chain structure of Cent-I in solution closely related to X-ray structure of native PPDK, three-dimensional structure calculated by different methods, topology of secondary structure indicated [Clostridium] symbiosum

Synonyms

Synonyms Comment Organism
PPDK
-
[Clostridium] symbiosum
pyruvate phosphate dikinase
-
[Clostridium] symbiosum

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
additional information
-
additional information turnover reactions of ATP and phosphate using equal concentrations of central domain protein Cent-I (PPDK central domain construct of residues 381-512-I) and the N-terminal domain protein Tem-340 does not produce the expected products [Clostridium] symbiosum