BRENDA - Enzyme Database show

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product

Boughton, B.; Dobson, R.; Hutton, C.; Proteins 80, 2117-2122 (2012)

Data extracted from this reference:

Application
EC Number
Application
Commentary
Organism
4.3.3.7
drug development
the enzyme is an attractive target for the design and synthesis of herbicides and antibiotics
Escherichia coli
Cloned(Commentary)
EC Number
Commentary
Organism
4.3.3.7
recombinant enzyme expression in Escherichia coli strain XL-1 Blue using plasmid pJG001
Escherichia coli
Crystallization (Commentary)
EC Number
Crystallization
Organism
4.3.3.7
purified enzyme in complex with pyruvate and substrate analogue succinic acid semialdehyde, hanging drop vapor diffusion method, mixing of 0.003 ml of 8 mg/mL protein in 20 mM Tris-HCl, pH 8.0, with 0.0012 ml of precipitant solution containing 1.8 M K2HPO4, pH 10, and 0.0006 ml of N-octyl-beta-R-glucopyranoside 6% w/v, 4°C, 3-4 days, soaking in cryoprotectant solution containing 1.8 M K2HPO4, pH 10, glycerol 20% v/v, and 120 mM succinic acid semialdehyde and 40 mM pyruvate, X-ray diffraction structure determination and analysis at 2.3 A resolution
Escherichia coli
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
Escherichia coli
-
(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
Escherichia coli
P0A6L2
-
-
Purification (Commentary)
EC Number
Commentary
Organism
4.3.3.7
recombinant enzyme 5.7fold from Escherichia coli strain XL-1 Blue
Escherichia coli
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
the enzyme-catalyzed reaction is initiated by condensation of pyruvate with an active site lysine residue (Lys161 in Escherichia coli DHDPS) forming a Schiff base, ping-pong kinetic reaction mechanism via enamine intermediate, overview
Escherichia coli
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
-
730908
Escherichia coli
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
4.3.3.7
homotetramer
the enzyme shows the typical homotetrameric form exhibited by bacterial DHDPS enzymes, present as a dimer of tight dimers. Each monomer consists of an N-terminal domain (residues 1-224) showing a parallel (beta/alpha)8-barrel (TIM barrel) motif. The smaller C-terminal domain, residues 224-292, is comprised of three alpha-helices
Escherichia coli
Application (protein specific)
EC Number
Application
Commentary
Organism
4.3.3.7
drug development
the enzyme is an attractive target for the design and synthesis of herbicides and antibiotics
Escherichia coli
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
recombinant enzyme expression in Escherichia coli strain XL-1 Blue using plasmid pJG001
Escherichia coli
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.3.3.7
purified enzyme in complex with pyruvate and substrate analogue succinic acid semialdehyde, hanging drop vapor diffusion method, mixing of 0.003 ml of 8 mg/mL protein in 20 mM Tris-HCl, pH 8.0, with 0.0012 ml of precipitant solution containing 1.8 M K2HPO4, pH 10, and 0.0006 ml of N-octyl-beta-R-glucopyranoside 6% w/v, 4°C, 3-4 days, soaking in cryoprotectant solution containing 1.8 M K2HPO4, pH 10, glycerol 20% v/v, and 120 mM succinic acid semialdehyde and 40 mM pyruvate, X-ray diffraction structure determination and analysis at 2.3 A resolution
Escherichia coli
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
Escherichia coli
-
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
recombinant enzyme 5.7fold from Escherichia coli strain XL-1 Blue
Escherichia coli
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
-
730908
Escherichia coli
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
4.3.3.7
homotetramer
the enzyme shows the typical homotetrameric form exhibited by bacterial DHDPS enzymes, present as a dimer of tight dimers. Each monomer consists of an N-terminal domain (residues 1-224) showing a parallel (beta/alpha)8-barrel (TIM barrel) motif. The smaller C-terminal domain, residues 224-292, is comprised of three alpha-helices
Escherichia coli
General Information
EC Number
General Information
Commentary
Organism
4.3.3.7
metabolism
the enzyme catalyses the first committed step in the lysine biosynthesis pathway, the condensation of pyruvate and (S)-aspartate semialdehyde to form (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid
Escherichia coli
4.3.3.7
additional information
the catalytic site of DHDPS is situated at the C-terminal end of the TIM barrel where the pyruvate-binding residue, Lys161, lies in a solvent-accessible cleft with Arg138 capping the binding site. One-half of the active site is blocked by binding interactions of another monomer
Escherichia coli
General Information (protein specific)
EC Number
General Information
Commentary
Organism
4.3.3.7
metabolism
the enzyme catalyses the first committed step in the lysine biosynthesis pathway, the condensation of pyruvate and (S)-aspartate semialdehyde to form (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid
Escherichia coli
4.3.3.7
additional information
the catalytic site of DHDPS is situated at the C-terminal end of the TIM barrel where the pyruvate-binding residue, Lys161, lies in a solvent-accessible cleft with Arg138 capping the binding site. One-half of the active site is blocked by binding interactions of another monomer
Escherichia coli