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Literature summary for 5.1.1.7 extracted from

  • Hor, L.; Dobson, R.; Downton, M.; Wagner, J.; Hutton, C.; Perugini, M.
    Dimerization of bacterial diaminopimelate epimerase is essential for catalysis (2013), J. Biol. Chem., 288, 9238-9248.
    View publication on PubMedView publication on EuropePMC

Application

Application Comment Organism
drug development the enzyme is a promising antimicrobial target Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) Organism
wild-type and Y268A mutant enzymes, hanging drop vapor diffusion method, 0.002 ml of 8.0 mg/ml protein in 20 mM Tris, 5 mM DTT, and 5 mM tris(2-carboxyethyl)phosphine, pH 7.8, are mixed with 0.002 ml of precipitant solution containing 0.2 M sodium iodide, 18% w/v PEG 3350, 0.1 M Bis-Tris propane, pH 6.5, 5 mM diaminoheptanedioate, 20°C, cryoprotectant is glycerol 20% v/v, X-ray diffraction structure determination and analysis at 2.0-2.05 A resolution Escherichia coli

Protein Variants

Protein Variants Comment Organism
Y268A site-directed mutagenesis, the monomeric mutant is catalytically inactive Escherichia coli

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
31031
-
2 * 31031, recombinant enzyme, mass spectrometry Escherichia coli
61300
-
recombinant enzyme, analytical ultracentrifugation Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
LL-2,6-Diaminoheptanedioate Escherichia coli
-
meso-Diaminoheptanedioate
-
r

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
gene dapF
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
LL-2,6-Diaminoheptanedioate
-
Escherichia coli meso-Diaminoheptanedioate
-
r

Subunits

Subunits Comment Organism
dimer 2 * 31031, recombinant enzyme, mass spectrometry Escherichia coli
More DAP epimerase from Escherichia coli exists as a functional dimer in solution and the crystal state, dimerization of bacterial diaminopimelate epimerase is essential for catalysis. Molecular dynamics simulations indicate that the DAP epimerase monomer is inherently more flexible than the dimer, suggesting that dimerization optimizes protein dynamics to support function. The dimer-monomer dissociation constant is 22 nM. The dimerization interfaceof the epimerase occurs between the N-terminal domains of the two monomers Escherichia coli

Synonyms

Synonyms Comment Organism
DAP epimerase
-
Escherichia coli

Cofactor

Cofactor Comment Organism Structure
additional information the enzyme is independent of pyridoxal 5'-phosphate Escherichia coli

General Information

General Information Comment Organism
evolution the enzyme is a member of the pyridoxal 5'-phosphate-independent racemase family of enzymes Escherichia coli
metabolism meso-diaminopimelate is a biosynthetic precursor of L-lysine in bacteria Escherichia coli
additional information dimerization of bacterial diaminopimelate epimerase is essential for catalysis, the enzyme exists in an open, active conformation. The active site of the enzyme resides in a cleft between the two domains with each domain contributing one of the cysteine residues important for catalysis Escherichia coli
physiological function diaminopimelate epimerase is involved in the biosynthesis of meso-DAP and lysine, which are important precursors for the synthesis of peptidoglycan, housekeeping proteins, and virulence factors in bacteria Escherichia coli