BRENDA - Enzyme Database show

Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein

Rice, E.A.; Bannon, G.A.; Glenn, K.C.; Jeong, S.S.; Sturman, E.J.; Rydel, T.J.; Arch. Biochem. Biophys. 480, 111-121 (2008)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
4.3.3.7
expressed in Escherichia coli STBL2, pET23b vector
Corynebacterium glutamicum
Crystallization (Commentary)
EC Number
Crystallization
Organism
4.3.3.7
hanging drop method, data collection and refinement statistics, refinement resolution originally extended to 3.0 A, gradually increased to 2.5 A, and finally to 2.2 A, structural similarities to other dihydrodipicolinate synthase
Corynebacterium glutamicum
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
4.3.3.7
3-Bromopyruvate
competitive inhibition, pyruvate as varied substrate
Corynebacterium glutamicum
4.3.3.7
L-aspartate
competitive inhibition, L-aspartate 4-semialdehyde as varied substrate
Corynebacterium glutamicum
4.3.3.7
L-aspartate 4-semialdehyde
uncompetitive inhibition by high concentrations of, no overcome by increasing pyruvate concentrations from 5 to 15 mM
Corynebacterium glutamicum
4.3.3.7
L-lysine
lack of feedback inhibition, not regulated under normal physiological conditions
Corynebacterium glutamicum
4.3.3.7
oxaloacetate
non-competitive inhibition, pyruvate as varied substrate
Corynebacterium glutamicum
4.3.3.7
Succinic semialdehyde
uncompetitive inhibition, L-aspartate 4-semialdehyde as varied substrate
Corynebacterium glutamicum
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.3.3.7
0.32
-
pyruvate
2.5 mM pyruvate replaced by 0.1-2 mM, no substrate inhibition observed at high concentrations of pyruvate
Corynebacterium glutamicum
4.3.3.7
0.63
-
L-aspartate 4-semialdehyde
reaction mixture includes 100 mM Tris-HCl, 2.5 mM pyruvate, 0.05-0.1 microg dihydrodipicolinate synthase and 0.2 mM NADPH, from 5.6 to 22.4 mM plots deviate from typical Michaelis-Menten kinetics, increased concentration fits an uncompetitive substrate inhibition model
Corynebacterium glutamicum
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
4.3.3.7
73000
-
approximating the size of two DHDPS proteins interacting to form a dimer
Corynebacterium glutamicum
4.3.3.7
158000
-
native protein, gel filtration, homotetramer predicted
Corynebacterium glutamicum
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.3.3.7
Corynebacterium glutamicum
P19808
-
-
Purification (Commentary)
EC Number
Commentary
Organism
4.3.3.7
gel filtration, SDS-PAGE
Corynebacterium glutamicum
Source Tissue
EC Number
Source Tissue
Commentary
Organism
Textmining
Specific Activity [micromol/min/mg]
EC Number
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
4.3.3.7
additional information
-
structure in vicinity of the putative binding site for S-lysine indicates that the allosteric binding site in the Escherichia coli dihydrodipicolinate synthase does not exist in the enzyme of Corynebacterium glutamicum, difference of three non-conservative amino acids substitutions, explains lack of feedback inhibition by lysine in Corynebacterium glutamicum
Corynebacterium glutamicum
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.3.3.7
L-aspartate 4-semialdehyde + pyruvate
lysine insensitivity of dihydrodipicolinate synthase analyzed, catalytic lysine residue forms a Schiff base adduct with pyruvate, active site lysine residues (K176a, K176b)
690628
Corynebacterium glutamicum
dihydrodipicolinate + H2O
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
4.3.3.7
homotetramer
ribbons rendition of homotetramer in the crystal lattice shown
Corynebacterium glutamicum
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.3.3.7
213
-
L-aspartate 4-semialdehyde
-
Corynebacterium glutamicum
IC50 Value
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
4.3.3.7
660
-
5 mM pyruvate, addition of 0-716 mM lysine, lack of feedback inhibition
Corynebacterium glutamicum
L-lysine
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
expressed in Escherichia coli STBL2, pET23b vector
Corynebacterium glutamicum
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.3.3.7
hanging drop method, data collection and refinement statistics, refinement resolution originally extended to 3.0 A, gradually increased to 2.5 A, and finally to 2.2 A, structural similarities to other dihydrodipicolinate synthase
Corynebacterium glutamicum
IC50 Value (protein specific)
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
4.3.3.7
660
-
5 mM pyruvate, addition of 0-716 mM lysine, lack of feedback inhibition
Corynebacterium glutamicum
L-lysine
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
4.3.3.7
3-Bromopyruvate
competitive inhibition, pyruvate as varied substrate
Corynebacterium glutamicum
4.3.3.7
L-aspartate
competitive inhibition, L-aspartate 4-semialdehyde as varied substrate
Corynebacterium glutamicum
4.3.3.7
L-aspartate 4-semialdehyde
uncompetitive inhibition by high concentrations of, no overcome by increasing pyruvate concentrations from 5 to 15 mM
Corynebacterium glutamicum
4.3.3.7
L-lysine
lack of feedback inhibition, not regulated under normal physiological conditions
Corynebacterium glutamicum
4.3.3.7
oxaloacetate
non-competitive inhibition, pyruvate as varied substrate
Corynebacterium glutamicum
4.3.3.7
Succinic semialdehyde
uncompetitive inhibition, L-aspartate 4-semialdehyde as varied substrate
Corynebacterium glutamicum
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.3.3.7
0.32
-
pyruvate
2.5 mM pyruvate replaced by 0.1-2 mM, no substrate inhibition observed at high concentrations of pyruvate
Corynebacterium glutamicum
4.3.3.7
0.63
-
L-aspartate 4-semialdehyde
reaction mixture includes 100 mM Tris-HCl, 2.5 mM pyruvate, 0.05-0.1 microg dihydrodipicolinate synthase and 0.2 mM NADPH, from 5.6 to 22.4 mM plots deviate from typical Michaelis-Menten kinetics, increased concentration fits an uncompetitive substrate inhibition model
Corynebacterium glutamicum
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
4.3.3.7
73000
-
approximating the size of two DHDPS proteins interacting to form a dimer
Corynebacterium glutamicum
4.3.3.7
158000
-
native protein, gel filtration, homotetramer predicted
Corynebacterium glutamicum
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
gel filtration, SDS-PAGE
Corynebacterium glutamicum
Source Tissue (protein specific)
EC Number
Source Tissue
Commentary
Organism
Textmining
Specific Activity [micromol/min/mg] (protein specific)
EC Number
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
4.3.3.7
additional information
-
structure in vicinity of the putative binding site for S-lysine indicates that the allosteric binding site in the Escherichia coli dihydrodipicolinate synthase does not exist in the enzyme of Corynebacterium glutamicum, difference of three non-conservative amino acids substitutions, explains lack of feedback inhibition by lysine in Corynebacterium glutamicum
Corynebacterium glutamicum
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
L-aspartate 4-semialdehyde + pyruvate
lysine insensitivity of dihydrodipicolinate synthase analyzed, catalytic lysine residue forms a Schiff base adduct with pyruvate, active site lysine residues (K176a, K176b)
690628
Corynebacterium glutamicum
dihydrodipicolinate + H2O
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
4.3.3.7
homotetramer
ribbons rendition of homotetramer in the crystal lattice shown
Corynebacterium glutamicum
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.3.3.7
213
-
L-aspartate 4-semialdehyde
-
Corynebacterium glutamicum