Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
(2S,6S)-2,6-diaminoheptanedioate
meso-diaminoheptanedioate
-
Substrates: -
Products: -
?
DL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
-
Substrates: rapid elimination, enamine product is formed which spontaneously cyclizes to tetrahydrodipicolinic acid
Products: -
?
LL-2,6-Diaminoheptanedioate
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
LL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
-
Substrates: slow elimination of HF
Products: -
?
LL-oxa-diaminopimelic acid
meso-oxa-diaminopimelic acid
Substrates: -
Products: -
?
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
additional information
?
-
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme active in two of three possible pathways for synthesis of L-Lys, acetyltransferase pathway and succinyltransferase pathway. Not active in D-diaminopimelate dehydrogenase variant
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme of Lys biosynthesis
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme of Lys biosynthesis
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Chlamydomonas sp.
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: r, between 25°C and 45°C at pH 7.0, the equilibrium mixture contains 65% meso-isomer and 35% LL-isomer
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
-
Substrates: stereo-inversion
Products: -
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
Substrates: stereo-conversion, the product complex (Enzyme/meso-diaminopimelate) is less stable than the reactant complex (Enzyme/LL-diaminopimelate)
Products: -
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
Substrates: stereo-inversion
Products: the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
Substrates: stereo-inversion
Products: the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
?
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
r
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
r
additional information
?
-
Substrates: ligand binding to a cleft between the two domains of the enzyme is accompanied by domain closure with strictly conserved cysteine residues, Cys99 and Cys254, positioned to perform acid/base catalysis via a carbanion stabilization mechanism on the stereogenic alpha-carbon atom of the amino acid. Stereochemical control in catalysis is achieved by means of a highly symmetric catalytic site that can accommodate both the L and D stereogenic centers of DAP at the proximal site, whereas specific interactions at the distal site require only the L configuration
Products: -
?
additional information
?
-
-
Substrates: ligand binding to a cleft between the two domains of the enzyme is accompanied by domain closure with strictly conserved cysteine residues, Cys99 and Cys254, positioned to perform acid/base catalysis via a carbanion stabilization mechanism on the stereogenic alpha-carbon atom of the amino acid. Stereochemical control in catalysis is achieved by means of a highly symmetric catalytic site that can accommodate both the L and D stereogenic centers of DAP at the proximal site, whereas specific interactions at the distal site require only the L configuration
Products: -
?
additional information
?
-
-
Substrates: Chlamydia trachomatis dapF encodes a bifunctional enzyme capable of both D-glutamate racemase, EC 5.1.1.3, and diaminopimelate epimerase activities. DAP and glutamate appear to be competitive substrates, indicating that they share an active site despite the racemase reaction requiring the pyridoxal 5'-phosphate cofactor
Products: -
?
additional information
?
-
Substrates: no activity with DD-2,6-diaminoheptanedioate. Development of a simple method using thin-layer chromatography, in methanol/water (64:36) and with ninhydrin detection, and chiral column chromatography to allow preparation of pure diaminopimelate isomers and detect products, respectively, overview
Products: -
?
additional information
?
-
Substrates: no activity with DD-2,6-diaminoheptanedioate. Development of a simple method using thin-layer chromatography, in methanol/water (64:36) and with ninhydrin detection, and chiral column chromatography to allow preparation of pure diaminopimelate isomers and detect products, respectively, overview
Products: -
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
LL-2,6-Diaminoheptanedioate
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
additional information
?
-
-
Substrates: Chlamydia trachomatis dapF encodes a bifunctional enzyme capable of both D-glutamate racemase, EC 5.1.1.3, and diaminopimelate epimerase activities. DAP and glutamate appear to be competitive substrates, indicating that they share an active site despite the racemase reaction requiring the pyridoxal 5'-phosphate cofactor
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme active in two of three possible pathways for synthesis of L-Lys, acetyltransferase pathway and succinyltransferase pathway. Not active in D-diaminopimelate dehydrogenase variant
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme of Lys biosynthesis
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme of Lys biosynthesis
Products: -
?
LL-2,6-Diaminoheptanedioate
?
-
Substrates: enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
Products: -
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Substrates: -
Products: -
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
-
Substrates: stereo-inversion
Products: -
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
Substrates: stereo-conversion, the product complex (Enzyme/meso-diaminopimelate) is less stable than the reactant complex (Enzyme/LL-diaminopimelate)
Products: -
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
Substrates: stereo-inversion
Products: the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
Substrates: stereo-inversion
Products: the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
evolution
-
the enzyme is a member of the pyridoxal 5'-phosphate-independent racemase family of enzymes
evolution
-
the enzyme is a member of the pyridoxal 5'-phosphate-independent racemase family of enzymes
metabolism
-
meso-diaminopimelate is a biosynthetic precursor of L-lysine in bacteria
metabolism
-
meso-diaminopimelate is a biosynthetic precursor of L-lysine in bacteria
metabolism
-
diaminopimelate epimerase (DapF) catalyzes the final step in the synthesis of meso-diaminopimelate, an amino acid unique to peptidoglycan, and synthesizes D-glutamate, EC 5.1.1.3
metabolism
the enzyme is involved in L-lysine biosynthesis, where it converts LL-diaminopimelate (LL-DAP) into DL-DAP. In the succinylase pathway, LL-diaminopimelate is synthesized from THDP by succinylation, transamination, and desuccinylation steps, LL-DAP is converted to DL-DAP by the action of DAP epimerase. In contrast, in the mDAP dehydrogenase pathway, DAP dehydrogenase converts THDP into DL-DAP in one step, DAP decarboxylase subsequently catalyzes the decarboxylation of DL-DAP to form L-lysine
metabolism
-
the enzyme is involved in L-lysine biosynthesis, where it converts LL-diaminopimelate (LL-DAP) into DL-DAP. In the succinylase pathway, LL-diaminopimelate is synthesized from THDP by succinylation, transamination, and desuccinylation steps, LL-DAP is converted to DL-DAP by the action of DAP epimerase. In contrast, in the mDAP dehydrogenase pathway, DAP dehydrogenase converts THDP into DL-DAP in one step, DAP decarboxylase subsequently catalyzes the decarboxylation of DL-DAP to form L-lysine
-
physiological function
enzyme belongs to the group of isomerases which are capable of inverting the absolute configuration of a carbon atom in substrates containing one (racemases) or more stereocenters
physiological function
-
enzyme is a member of the PLP-independent amino-acid racemases, it catalyzes the penultimate step of lysine biosynthesis in bacteria and plants
physiological function
synthesis of L-lysine
physiological function
-
(2R,6S)-2,6-diaminopimelic acid, i.e. meso-diaminopimelate, in the pentapeptide of cell wall peptidoglycan provides the attachment site for the inner or outer membrane to peptidoglycan
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
physiological function
diaminopimelate isomers are not only intermediates of the lysine biosynthesis diaminopimelate pathway but also essential components of bacterial peptidoglycan
physiological function
redox-mediated modification of cellular proteins confers a respose to changes in the environmental redox potential. CgDapF is regulated by redox-switch modulation, via reversible disulfide bond formation
physiological function
-
redox-mediated modification of cellular proteins confers a respose to changes in the environmental redox potential. CgDapF is regulated by redox-switch modulation, via reversible disulfide bond formation
-
physiological function
-
synthesis of L-lysine
-
physiological function
-
diaminopimelate isomers are not only intermediates of the lysine biosynthesis diaminopimelate pathway but also essential components of bacterial peptidoglycan
-
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
additional information
C83 and C221 are catalytic residues
additional information
-
C83 and C221 are catalytic residues
additional information
-
the structure of Chlamydia DAP epimerase exhibits significant remodeling in the substrate-binding pocket, overview
additional information
-
C83 and C221 are catalytic residues
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 0.001 ml of 14 mg/ml protein in 20 mM HEPES, pH 7.0, 100 mM NaCl, and 5 mM DTT, with 0.001 ml of reservoir solution containing 2 M ammonium sulfate, 0.1 M sodium HEPES, pH 7.5, and 4.9-5.1% PEG 400, equilibration against reservoir solution, 25% v/v PEG 400 as a cryoprotectant, method optimization, X-ray diffraction structure determination and analysis at 1.9 A resolution
-
in complex with two different isomers of inhibitor 2-(4-amino-4-carboxybutyl)-aziridine-2-carboxylate, at 1.95 and 2.3 A resolution. Ligand binding to a cleft between the two domains of the enzyme is accompanied by domain closure with strictly conserved cysteine residues, Cys99 and Cys254, positioned to perform acid/base catalysis via a carbanion stabilization mechanism on the stereogenic alpha-carbon atom of the amino acid. Stereochemical control in catalysis is achieved by means of a highly symmetric catalytic site that can accommodate both the L and D stereogenic centers of DAP at the proximal site, whereas specific interactions at the distal site require only the L configuration
purified enzyme CgDapF in both oxidized and reduced forms, selenium-substituted crystal, hanging drop vapor diffusion method, mixing of 0.001 ml of 40 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution containing 1.6 M ammonium sulfate, and 0.1 M Bis-Tris, pH 5.0, for the oxidized enzyme form and 1.4 M sodium phosphate monobasic/0.9 M potassium phosphate dibasic, 0.1 M CAPS, pH 10.0, 0.2 M lithium sulfate, and 1 mM 1,4-DTT for the reduced enzyme form, the crystals of CgDapF in complex with DL-DAP are crystallized in the condition of 1.3 M sodium citrate, 0.1 M CHES, pH 9.0, and 10 mM DAP isomer, equilibration against 0.5 ml, 20°C, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution, single-wavelength anomalous dispersion method, molecular replacement
by using the sitting-drop vapour-diffusion method with droplets consisting of 150 nl protein solution and 150 nl reservoir solution, conditions that yield crystals are replicated using the hanging-drop vapourdiffusion method with drops containing 0.002 ml protein solution and 0.002 ml precipitant solution, crystals are obtained in space group P41212 and diffract to 2.0 A resolution, with unit-cell parameters a = b = 89.4, c = 179.6 A
-
sitting drop vapour diffusion method, 2.5 A resolution
-
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
-
co-crystals of the inhibitors LL- and DL-aziridino diaminopimelic acid with diaminopimelate epimerase from Haemophilus influenzae are grown at room temperature by the hanging-drop vapor-diffusion method. Crystals of both complexes are obtained in 2.8 M sodium acetate /0.1 M Hepes (pH 7.0) at a protein concentration of approx. 10 mg/ml in 25 mM Hepes, 5 mM DTT (pH 8.0)
comparisons of the mutant structures with the structures of the AziDAP inhibitor-bound form reveal that the enzyme adopts an open conformation in the absence of substrates or inhibitors with the two active site cysteines existing as a thiolthiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base
crystal structures of diaminopimelate epimerase from Haemophilus influenzae with two different isomers of the irreversible inhibitor and substrate mimic aziridino diaminopimelic acid at 1.35- and 1.70-A resolution are analysed. These structures permit a detailed description of this pyridoxal 5-phosphate-independent amino acid racemase active site and delineate the electrostatic interactions that control the exquisite substrate selectivity of DAP epimerase. Moreover, the active site shows how deprotonation of the substratesnonacidic hydrogen at the alpha-carbon by a seemingly weakly basic cysteine residue is facilitated by interactions with two buried alpha-helices
crystallization of C73S and C217S mutant diaminopimelate epimerase enzymes of Haemophilus influenzae are obtained by the hanging-drop vapor diffusion method and submitted to X-ray structure analysis
hanging-drop vapour-diffusion method, space group C222(1), unit cell parameters a = 98.64 A, b = 113.87 A, c = 64.48 A, 1.75 A resolution
-
crystal structure of the ligand-free form refines to a resolution of 2.6 A, 2.5 mM dithiothreitol is present in the crystal drop
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
C221A
site-directed mutagenesis, nearly inactive mutant
C83A
site-directed mutagenesis, nearly inactive mutant
E212A
site-directed mutagenesis, nearly inactive mutant
N159A
site-directed mutagenesis, nearly inactive mutant
N15A
site-directed mutagenesis, nearly inactive mutant
N194A
site-directed mutagenesis, nearly inactive mutant
N74A
site-directed mutagenesis, nearly inactive mutant
N85A
site-directed mutagenesis, nearly inactive mutant
R213A
site-directed mutagenesis, nearly inactive mutant
T223A
site-directed mutagenesis, nearly inactive mutant
N159A
-
site-directed mutagenesis, nearly inactive mutant
-
N74A
-
site-directed mutagenesis, nearly inactive mutant
-
N85A
-
site-directed mutagenesis, nearly inactive mutant
-
R213A
-
site-directed mutagenesis, nearly inactive mutant
-
T223A
-
site-directed mutagenesis, nearly inactive mutant
-
Y268A
-
site-directed mutagenesis, the monomeric mutant is catalytically inactive
C217A
-
mutant enzyme is inactive as epimerase, catalyzes elimination of HF via abstraction of the C-2 hydrogen from L,L-3-fluoro-2,6-diaminopimelate, incapable of catalyzing HF elimination from D,L-3-fluoro-2,6-diaminopimelate
C217S
-
catalyzes epimerization of L,L-diaminopimelate at 2% of the activity of the wild-type enzyme,catalyzes HF elimination from L,L-3-fluoro-2,6-diaminopimelate and D,L-3-fluoro-2,6-diaminopimelate
C73A
-
mutant enzyme is inactive as epimerase, catalyzes elimination of HF via abstraction of the C-2 hydrogen. Mutant enzyme is able to rapidly catalyze elimination of the D,L-3-fluoro-2,6-diaminopimelate and is unable to catalyze elimination with the L,L-3-fluoro-2,6-diaminopimelate
C73S
-
epimerization of L,L-diaminopimelate at 3% of the activity of the wild-type enzyme, catalyzes HF elimination from L,L-3-fluoro-2,6-diaminopimelate and D,L-3-fluoro-2,6-diaminopimelate
C226A
complete loss of activity
C226S
severely compromised catalytic efficiency
C87A
complete loss of activity
C87S
severely compromised catalytic efficiency despite decrease in Km value
C226A
-
complete loss of activity
-
C226S
-
severely compromised catalytic efficiency
-
C87A
-
complete loss of activity
-
C87S
-
severely compromised catalytic efficiency despite decrease in Km value
-
C73S/C217S
-
mutant enzyme is inactive as epimerase, slow elimination of HF from D,L-3-fluoro-2,6-diaminopimelate and L,L-3-fluoro-2,6-diaminopimelate
C73S/C217S
in order to prevent C73 and C217 of DAP epimerase from oxidation to a disulfide prior to crystallization, DAP epimerase mutants C73S and C217S from Haemophilus influenzae are generated by site-directed mutagenesis
additional information
-
a recombinant DapF is generated consisting of silent mutation of the first 10 codons of the open reading frame. single nucleotide substitutions are incorporated without changing product composition in the first 30 nucleotides of the dapF open reading frame,in order to disrupt any secondary structure-promoting sequences present. this significantly increases the yield of the enzyme
additional information
-
a recombinant DapF is generated consisting of silent mutation of the first 10 codons of the open reading frame. single nucleotide substitutions are incorporated without changing product composition in the first 30 nucleotides of the dapF open reading frame,in order to disrupt any secondary structure-promoting sequences present. this significantly increases the yield of the enzyme
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
Adams, E.
Amino acid racemases and epimerases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
6
479-507
1972
Escherichia coli, Priestia megaterium
-
brenda
Withe, P.J.; Lejeune, B.; Work, E.
Assay and properties of diaminopimelate epimerase from Bacillus megaterium
Biochem. J.
113
589-601
1969
Priestia megaterium
brenda
Tyagi, V.V.S.; Henke, R.R.; Farkas, W.R.
Occurence of diaminopimelic epimerase in maize
Biochim. Biophys. Acta
719
363-369
1982
Zea mays
-
brenda
Bartlett, A.T.M.; White, P.J.
Species of Bacillus that make a vegetative peptidoglycan containing lysine lack diaminopimelate epimerase but have diaminopimelate dehydrogenase
J. Gen. Microbiol.
131
2145-2152
1985
Brevibacillus laterosporus, Geobacillus stearothermophilus, Niallia circulans, no activity in Bacillus globisporus, no activity in Bacillus pasteurii, no activity in Bacillus sphaericus, Paenibacillus macerans, Paenibacillus polymyxa, Priestia megaterium, Virgibacillus pantothenticus
-
brenda
Wiseman, J.S.; Nichols, J.S.
Purification and properties of diaminopimelic acid epimerase from Escherichia coli
J. Biol. Chem.
259
8907-8914
1984
Escherichia coli
brenda
Richaud, C.; Higgins, W.; Mengin-Lecreulx, D.; Stragier, P.
Molecular cloning, characterization, and chromosomal localization of dapF, the Escherichia coli gene for diaminopimelate epimerase
J. Bacteriol.
169
1454-1459
1987
Escherichia coli
brenda
Chatterjee, S.P.; White, P.J.
Activities and regulation of the enzymes of lysine biosynthesis in a lysine-excreting strain of Bacillus megaterium
J. Gen. Microbiol.
128
1073-1081
1982
Priestia megaterium
-
brenda
Misono, H.; Soda, K.
Determination of meso-alpha,epsilon-diaminopimelate with meso-alpha,epsilon-diaminopimelate D-dehydrogenase
Agric. Biol. Chem.
44
2125-2128
1980
Bacteria
-
brenda
Baumann, R.J.; Bohme, E.H.; Wiseman, J.S.; Vaal, M.; Nichols, J.S.
Inhibition of Escherichia coli growth and diaminopimelic acid epimerase by 3-chlorodiaminopimelic acid
Antimicrob. Agents Chemother.
32
1119-1123
1988
Escherichia coli
brenda
Lam, L.K.P.; Arnold, L.D.; Kalantar, T.H.; Kelland, J.G.; Lane-Bell, P.M.; Palcic, M.M.; Pickard, M.A.; Vederas, J.C.
Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate dehydrogenase and LL-diaminopimelate epimerase
J. Biol. Chem.
263
11814-11819
1988
Escherichia coli
brenda
Gerhart, F.; Higgins, W.; Tardif, C.; Ducep, J.B.
2-(4-Amino-4-carboxybutyl)aziridine-2-carboxylic acid. A potent irreversible inhibitor of diaminopimelic acid epimerase. Spontaneous formation from alpha-(halomethyl)diaminopimelic acids
J. Med. Chem.
33
2157-2162
1990
Escherichia coli
brenda
Weir, A.N.C.; Bucke, C.; Holt, G.; Lilly, M.D.; Bull, A.T.
A high-performance liquid chromatography method for the simultaneous assay of diaminopimelate epimerase and decarboxylase
Anal. Biochem.
180
298-302
1989
Bacillus subtilis
brenda
Gelb, M.H.; Lin, Y.; Pickard, M.A.; Song, Y.; Vederas, J.C.
Synthesis of 3-fluorodiaminopimelic acid isomers as inhibitors of diaminopimelate epimerase: stereocontrolled enzymatic elimination of hydrogen fluoride
J. Am. Chem. Soc.
112
4932-4942
1990
Escherichia coli
-
brenda
Abbott, S.D.; Lane-Bell, P.; Sidhu, K.P.S.; Vederas, J.C.
Synthesis and testing of heterocyclic analogues of diaminopimelic acid (DAP) as inhibitors of DAP dehydrogenase and DAP epimerase
J. Am. Chem. Soc.
116
6513-6520
1994
Escherichia coli
-
brenda
Song, Y.; Niederer, D.; Lane-Bell, P.M.; Lam, L.K.P.; Crawley, S.; Palcic, M.M.; Pickard, M.A.; Pruess, D.L.; Vederas, J.C.
Stereospecific synthesis of phosphonate analogues of diaminopimelic acid (DAP), their interaction with DAP enzymes and antibacterial activity of peptide derivatives
J. Org. Chem.
59
5784-5793
1994
Escherichia coli
-
brenda
Schrumpf, B.; Schwarzer, A.; Kalinowski, J.; Puhler, A.; Eggeling, L.; Sahm, H.
A functionally split pathway for lysine synthesis in Corynebacterium glutamicum
J. Bacteriol.
173
4510-4516
1991
Bacillus subtilis, Corynebacterium glutamicum, Escherichia coli, no activity in Bacillus sphaericus
brenda
El-Waziry, A.M.; Onodera, R.
In vitro metabolism of the stereoisomers of 2,6-diaminopimelic acid by mixed rumen protozoa and bacteria
Curr. Microbiol.
33
306-311
1996
unclassified Bacteria
brenda
Chatterjee, S.P.; Singh, B.K.; Gilvarg, C.
Biosynthesis of lysine in plants: the putative role of meso-diaminopimelate dehydrogenase
Plant Mol. Biol.
26
285-290
1994
Chlamydomonas sp., Glycine max, Nicotiana tabacum, Zea mays
brenda
Chatterjee, M.
Lysine production by Brevibacterium linens and its mutants: activities and regulation of enzymes of the lysine biosynthetic pathway
Folia Microbiol. (Praha)
43
141-146
1998
Brevibacterium linens
brenda
Scapin, G.; Blanchard, J.S.
Enzymology of bacterial lysine biosynthesis
Adv. Enzymol. Relat. Areas Mol. Biol.
72
279-324
1998
Escherichia coli
brenda
Koo, C.W.; Sutherland, A.; Vederas, J.C.; Blanchard, J.S.
Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase
J. Am. Chem. Soc.
122
6122-6123
2000
Haemophilus influenzae
-
brenda
Caplan, J.F.; Zheng, R.; Blanchard, J.S.; Vederas, J.C.
Vinylogous amide analogues of diaminopimelic acid (DAP) as inhibitors of enzymes involved in bacterial lysine biosynthesis
Org. Lett.
2
3857-3860
2000
Escherichia coli
brenda
Lloyd, A.J.; Huyton, T.; Turkenburg, J.; Roper, D.I.
Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis
Acta Crystallogr. Sect. D
60
397-400
2004
Haemophilus influenzae
brenda
Grassick, A.; Sulzenbacher, G.; Roig-Zamboni, V.; Campanacci, V.; Cambillau, C.; Bourne, Y.
Crystal structure of E. coli YddE protein reveals a striking homology with diaminopimelate epimerase
Proteins
55
764-767
2004
Escherichia coli
brenda
Pillai, B.; Cherney, M.; Diaper, C.M.; Sutherland, A.; Blanchard, J.S.; Vederas, J.C.; James, M.N.
Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase
Biochem. Biophys. Res. Commun.
363
547-553
2007
Haemophilus influenzae (P44859), Haemophilus influenzae
brenda
Usha, V.; Dover, L.G.; Roper, D.L.; Lloyd, A.J.; Besra, G.S.
Use of a codon alteration strategy in a novel approach to cloning the Mycobacterium tuberculosis diaminopimelic acid epimerase
FEMS Microbiol. Lett.
262
39-47
2006
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
brenda
Brunetti, L.; Galeazzi, R.; Orena, M.; Bottoni, A.
Catalytic mechanism of l,l-diaminopimelic acid with diaminopimelate epimerase by molecular docking simulations
J. Mol. Graph. Model.
26
1082-1090
2008
Haemophilus influenzae
brenda
Pillai, B.; Cherney, M.M.; Diaper, C.M.; Sutherland, A.; Blanchard, J.S.; Vederas, J.C.; James, M.N.
Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target
Proc. Natl. Acad. Sci. USA
103
8668-8673
2006
Haemophilus influenzae (P44859), Haemophilus influenzae
brenda
Usha, V.; Dover, L.G.; Roper, D.L.; Besra, G.S.
Characterization of Mycobacterium tuberculosis diaminopimelic acid epimerase: paired cysteine residues are crucial for racemization
FEMS Microbiol. Lett.
280
57-63
2008
Mycobacterium tuberculosis (P9WP19), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WP19)
brenda
Pillai, B.; Moorthie, V.A.; van Belkum, M.J.; Marcus, S.L.; Cherney, M.M.; Diaper, C.M.; Vederas, J.C.; James, M.N.
Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for l-lysine biosynthesis
J. Mol. Biol.
385
580-594
2009
Arabidopsis thaliana (Q9LFG2), Arabidopsis thaliana
brenda
Usha, V.; Dover, L.G.; Roper, D.I.; Fuetterer, K.; Besra, G.S.
Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis
Acta Crystallogr. Sect. D
65
383-387
2009
Mycobacterium tuberculosis (P9WP19), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WP19)
brenda
Hor, L.; Dobson, R.; Dogovski, C.; Hutton, C.; Perugini, M.
Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli
Acta Crystallogr. Sect. F
66
37-40
2009
Escherichia coli
brenda
Stenta, M.; Calvaresi, M.; Alto, P.; Spinelli, D.; Garavelli, M.; Galeazzi, R.; Bottoni, A.
Catalytic mechanism of diaminopimelate epimerase: A QM/MM investigation
J. Chem. Theory Comput.
5
1915-1930
2009
Haemophilus influenzae (P44859)
brenda
Park, J.; Lee, W.; Song, J.; Kim, S.; Lee, J.; Cheong, C.; Kim, H.
Purification, crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from Acinetobacter baumannii
Acta Crystallogr. Sect. F
69
42-44
2013
Acinetobacter baumannii
brenda
Hor, L.; Dobson, R.; Downton, M.; Wagner, J.; Hutton, C.; Perugini, M.
Dimerization of bacterial diaminopimelate epimerase is essential for catalysis
J. Biol. Chem.
288
9238-9248
2013
Escherichia coli
brenda
Miura, H.; Hori, K.; Sasaki, Y.; Inahashi, Y.; Yagisawa, Y.; Fujita, N.; Omura, S.; Takahashi, Y.
Simple analytic method of diaminopimelate epimerase activity
J. Biosci. Bioeng.
116
253-255
2013
Kitasatospora setae (E4NI20), Kitasatospora setae KM-6054 (E4NI20)
brenda
Liechti, G.; Singh, R.; Rossi, P.; Gray, M.; Adams, N.; Maurelli, A.
Chlamydia trachomatis dapF encodes a bifunctional enzyme capable of both D-glutamate racemase and diaminopimelate epimerase activities
mBio
9
e00204-18
2018
Chlamydia trachomatis
brenda
Sagong, H.Y.; Kim, K.J.
Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase an enzyme involved in L-lysine biosynthesis
Sci. Rep.
7
42318
2017
Corynebacterium glutamicum (Q8NP73), Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 (Q8NP73)
brenda