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Crystal structure and in silico studies of dihydrodipicolinate synthase (DHDPS) from Aquifex aeolicus

Sridharan, U.; Ebihara, A.; Kuramitsu, S.; Yokoyama, S.; Kumarevel, T.; Ponnuraj, K.; Extremophiles 18, 973-985 (2014)

Data extracted from this reference:

Application
EC Number
Application
Commentary
Organism
4.3.3.7
drug development
the enzyme is an attractive target for rational antibiotic and herbicide design
Aquifex aeolicus
4.3.3.7
synthesis
the enzyme can be commercially exploited for high-yield production of (S)-lysine
Aquifex aeolicus
Cloned(Commentary)
EC Number
Commentary
Organism
4.3.3.7
gene dapA or Aq_1143, sequence comparisons, recombinant enzyme expression in Escherichia coli strain BL21-CodonPlus (DE3)-RIL
Aquifex aeolicus
Crystallization (Commentary)
EC Number
Crystallization
Organism
4.3.3.7
purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 21.8 mg/ml protein in 20 mM Tris-HCl at pH 8.0 and 0.2 M NaCl, with 0.001 ml of reservoir solution containing 4 M sodium phosphate, 0.1 M imidazole, and 0.2 M NaCl at pH 8.0, 18C, 1 week, X-ray diffraction structure determination and analysis at 1.90 A resolution, molecular replacement
Aquifex aeolicus
Engineering
EC Number
Amino acid exchange
Commentary
Organism
4.3.3.7
C139A
site-directed in silico mutation
Aquifex aeolicus
General Stability
EC Number
General Stability
Organism
4.3.3.7
molecular dynamics simulation to analyze the stability of the enzyme
Aquifex aeolicus
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
4.3.3.7
(S)-lysine
feedback inhibitor, docking study with enzyme crystals
Aquifex aeolicus
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
Aquifex aeolicus
-
(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
Aquifex aeolicus
O67216
gene dapA or Aq_1143
-
Purification (Commentary)
EC Number
Commentary
Organism
4.3.3.7
recombinant enzyme from Escherichia coli strain BL21-CodonPlus (DE3)-RIL by two different steps of anion exchange chromatography, dialysis, hydroxyapatite chromatography, another step of anion exchange chromatography, and gel filtration, to homogeneity
Aquifex aeolicus
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
reaction steps, overview
Aquifex aeolicus
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
-
729694
Aquifex aeolicus
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
4.3.3.7
tetramer
the overall quaternary structure of the enzyme consists of four crystallographically independent molecules (A, C, D, and E) forming dimer of dimers. The monomer exhibits a TIM barrel fold and comprises of 11 alpha helices built by 146 amino acids out of which the first 8 helices form the TIM barrel domain and remaining three helices present in the C-terminal. The monomer also has 10 beta strands composed of 42 amino acids. The enzyme molecule has two types of dimer interfaces, weak-dimer interface and tight-dimer interfaces, structure model, overview
Aquifex aeolicus
Temperature Stability [C]
EC Number
Temperature Stability Minimum [C]
Temperature Stability Maximum [C]
Commentary
Organism
4.3.3.7
90
-
the enzyme is stable up to, high-temperature molecular dynamics simulation of the wild-type and mutant enzymes
Aquifex aeolicus
Application (protein specific)
EC Number
Application
Commentary
Organism
4.3.3.7
drug development
the enzyme is an attractive target for rational antibiotic and herbicide design
Aquifex aeolicus
4.3.3.7
synthesis
the enzyme can be commercially exploited for high-yield production of (S)-lysine
Aquifex aeolicus
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.3.3.7
gene dapA or Aq_1143, sequence comparisons, recombinant enzyme expression in Escherichia coli strain BL21-CodonPlus (DE3)-RIL
Aquifex aeolicus
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.3.3.7
purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 21.8 mg/ml protein in 20 mM Tris-HCl at pH 8.0 and 0.2 M NaCl, with 0.001 ml of reservoir solution containing 4 M sodium phosphate, 0.1 M imidazole, and 0.2 M NaCl at pH 8.0, 18C, 1 week, X-ray diffraction structure determination and analysis at 1.90 A resolution, molecular replacement
Aquifex aeolicus
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
4.3.3.7
C139A
site-directed in silico mutation
Aquifex aeolicus
General Stability (protein specific)
EC Number
General Stability
Organism
4.3.3.7
molecular dynamics simulation to analyze the stability of the enzyme
Aquifex aeolicus
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
4.3.3.7
(S)-lysine
feedback inhibitor, docking study with enzyme crystals
Aquifex aeolicus
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
Aquifex aeolicus
-
(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 from Escherichia coli strain BL21-CodonPlus (DE3)-RIL by two different steps of anion exchange chromatography, dialysis, hydroxyapatite chromatography, another step of anion exchange chromatography, and gel filtration, to homogeneity
Aquifex aeolicus
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
-
729694
Aquifex aeolicus
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
4.3.3.7
tetramer
the overall quaternary structure of the enzyme consists of four crystallographically independent molecules (A, C, D, and E) forming dimer of dimers. The monomer exhibits a TIM barrel fold and comprises of 11 alpha helices built by 146 amino acids out of which the first 8 helices form the TIM barrel domain and remaining three helices present in the C-terminal. The monomer also has 10 beta strands composed of 42 amino acids. The enzyme molecule has two types of dimer interfaces, weak-dimer interface and tight-dimer interfaces, structure model, overview
Aquifex aeolicus
Temperature Stability [C] (protein specific)
EC Number
Temperature Stability Minimum [C]
Temperature Stability Maximum [C]
Commentary
Organism
4.3.3.7
90
-
the enzyme is stable up to, high-temperature molecular dynamics simulation of the wild-type and mutant enzymes
Aquifex aeolicus
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
Aquifex aeolicus
4.3.3.7
additional information
the enzyme has unique disulfide linkage which is critical for the stability of the enzyme tetramer, but is not conserved in homologous enzymes, molecular dynamics simulation of the native structure of the enzyme tetramer and dimeric units containing complexes of enzyme-pyruvate or enzyme-lysine, enzyme structure comparisons and ligand docking analysis, overview
Aquifex aeolicus
4.3.3.7
physiological function
the enzyme catalyzes a rate-limiting step in the (S)-lysine biosynthetic pathway, which is regulated by a feedback mechanism through lysine
Aquifex aeolicus
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
Aquifex aeolicus
4.3.3.7
additional information
the enzyme has unique disulfide linkage which is critical for the stability of the enzyme tetramer, but is not conserved in homologous enzymes, molecular dynamics simulation of the native structure of the enzyme tetramer and dimeric units containing complexes of enzyme-pyruvate or enzyme-lysine, enzyme structure comparisons and ligand docking analysis, overview
Aquifex aeolicus
4.3.3.7
physiological function
the enzyme catalyzes a rate-limiting step in the (S)-lysine biosynthetic pathway, which is regulated by a feedback mechanism through lysine
Aquifex aeolicus