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Dihydrodipicolinate synthase from Campylobacter jejuni: kinetic mechanism of cooperative allosteric inhibition and inhibitor-induced substrate cooperativity

Skovpen, Y.V.; Palmer, D.R.; Biochemistry 52, 5454-5462 (2013)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
4.3.3.7
gene dapA, expression of His-tagged enzyme in Escherichia coli strain XL1-Blue
Campylobacter jejuni
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
4.3.3.7
(S)-lysine
feedback inhibition, the tetrameric enzyme has two allosteric sites, each of which binds two molecules of lysine. Lysine binds highly cooperatively, and primarily to the F form of the enzyme during the ping-pong mechanism. (S)-Lysine is an uncompetitive partial inhibitor with respect to its first substrate, pyruvate, and a mixed partial inhibitor with respect to its second substrate, (S)-aspartate-4-semialdehyde
Campylobacter jejuni
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.3.3.7
additional information
-
additional information
kinetic modeling
Campylobacter jejuni
4.3.3.7
2.83
-
pyruvate
pH and temperature not specified in the publication
Campylobacter jejuni
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
4.3.3.7
(S)-aspartate-4-semialdehyde + pyruvate
Campylobacter jejuni
-
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.3.3.7
Campylobacter jejuni
-
gene dapA
-
Purification (Commentary)
EC Number
Commentary
Organism
4.3.3.7
recombinant His-tagged enzyme from Escherichia coli strain XL1-Blue by nickel affinity chromatography
Campylobacter jejuni
Reaction
EC Number
Reaction
Commentary
Organism
4.3.3.7
pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
ping-pong kinetic reaction mechanism
Campylobacter jejuni
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.3.3.7
(S)-aspartate-4-semialdehyde + pyruvate
-
729237
Campylobacter jejuni
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
4.3.3.7
(S)-aspartate-4-semialdehyde + pyruvate
(S)-aspartate-4-semialdehyde binds cooperatively in the presence of (S)-lysine with an average cooperativity coefficient n = 1.3, and the cooperativity of binding increases at near-KM concentrations of pyruvate with an average cooperativity coefficient n = 1.0
729237
Campylobacter jejuni
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
4.3.3.7
homotetramer
-
Campylobacter jejuni
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
4.3.3.7
additional information
-
additional information
(S)-lysine allosteric inhibition kinetics and mechanism, overview
Campylobacter jejuni
IC50 Value
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
4.3.3.7
0.065
-
pH and temperature not specified in the publication
Campylobacter jejuni
(S)-lysine
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
gene dapA, expression of His-tagged enzyme in Escherichia coli strain XL1-Blue
Campylobacter jejuni
IC50 Value (protein specific)
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
4.3.3.7
0.065
-
pH and temperature not specified in the publication
Campylobacter jejuni
(S)-lysine
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
4.3.3.7
(S)-lysine
feedback inhibition, the tetrameric enzyme has two allosteric sites, each of which binds two molecules of lysine. Lysine binds highly cooperatively, and primarily to the F form of the enzyme during the ping-pong mechanism. (S)-Lysine is an uncompetitive partial inhibitor with respect to its first substrate, pyruvate, and a mixed partial inhibitor with respect to its second substrate, (S)-aspartate-4-semialdehyde
Campylobacter jejuni
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
4.3.3.7
additional information
-
additional information
(S)-lysine allosteric inhibition kinetics and mechanism, overview
Campylobacter jejuni
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.3.3.7
additional information
-
additional information
kinetic modeling
Campylobacter jejuni
4.3.3.7
2.83
-
pyruvate
pH and temperature not specified in the publication
Campylobacter jejuni
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
4.3.3.7
(S)-aspartate-4-semialdehyde + pyruvate
Campylobacter jejuni
-
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
recombinant His-tagged enzyme from Escherichia coli strain XL1-Blue by nickel affinity chromatography
Campylobacter jejuni
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.3.3.7
(S)-aspartate-4-semialdehyde + pyruvate
-
729237
Campylobacter jejuni
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
4.3.3.7
(S)-aspartate-4-semialdehyde + pyruvate
(S)-aspartate-4-semialdehyde binds cooperatively in the presence of (S)-lysine with an average cooperativity coefficient n = 1.3, and the cooperativity of binding increases at near-KM concentrations of pyruvate with an average cooperativity coefficient n = 1.0
729237
Campylobacter jejuni
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
4.3.3.7
homotetramer
-
Campylobacter jejuni