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Information on EC 5.1.1.7 - diaminopimelate epimerase
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5.1.1.7 diaminopimelate epimeraseSpecify your search results
Word Map
- 5.1.1.7
-
meso-dap
-
immunophilins
-
racemase
- drug development
-
ll-dap
- meso-diaminopimelate
- fkbp-12
- rotamase
- analysis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
dap epimerase, diaminopimelic acid epimerase, mtdapf, dap-epimerase, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
CgDapF
DAP epimerase
DAP-epimerase
DapF
diaminopimelate epimerase
Diaminopimelic acid epimerase
Diaminopimelic epimerase
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Epimerase, diaminopimelate
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LL-Diaminopimelate epimerase
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-
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DAP epimerase
-
-
-
-
DAP epimerase
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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-
DAP-epimerase
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Diaminopimelic acid epimerase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
two-base mechanism for proton translocation. One, but not both, of the proton acceptor sites is a thiol
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-
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LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
molecular dynamics simulations show that the configuration of the distal carbon C–6 of L,L-DAP is critical for complex formation since both amino and carboxylate groups are involved in H–bonding interactions with the active site residues. Furthermore, the interactions occurring between the functional groups bonded to the C–2 and some residues of the binding cavity immobilize the ligand in a position appropriate for the epimerization reaction, i.e., exactly in the middle of the two catalytic residues Cys73 and Cys217 as confirmed by DFT (density-functional theory) quantum mechanical computation of the Michaelis complex
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LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
molecular mechanism of the enzyme, reversible disulfide bond formation at the active site of CgDapF and disulfide bond-mediated conformational change in CgDapF, domain movement in CgDapF, CgDapF is regulated by redox-switch modulation, via reversible disulfide bond formation, overview
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
molecular mechanism of the enzyme, reversible disulfide bond formation at the active site of CgDapF and disulfide bond-mediated conformational change in CgDapF, domain movement in CgDapF, CgDapF is regulated by redox-switch modulation, via reversible disulfide bond formation, overview
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
epimerization
epimerization
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-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
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SYSTEMATIC NAME
IUBMB Comments
LL-2,6-diaminoheptanedioate 2-epimerase
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CAS REGISTRY NUMBER
COMMENTARY
9024-22-0
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2S,6S)-2,6-diaminoheptanedioate
meso-diaminoheptanedioate
-
-
-
?
DL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
-
rapid elimination, enamine product is formed which spontaneously cyclizes to tetrahydrodipicolinic acid
-
?
LL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
-
slow elimination of HF
-
?
LL-2,6-Diaminoheptanedioate
?
-
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
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-
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LL-2,6-Diaminoheptanedioate
?
-
enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
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-
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LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
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r, between 25°C and 45°C at pH 7.0, the equilibrium mixture contains 65% meso-isomer and 35% LL-isomer
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LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
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r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
-
stereo-conversion, the product complex (Enzyme/meso-diaminopimelate) is less stable than the reactant complex (Enzyme/LL-diaminopimelate)
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-
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
-
stereo-inversion
the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
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?
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
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-
-
r
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
-
-
-
r
additional information
?
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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
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additional information
?
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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
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additional information
?
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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
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additional information
?
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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
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additional information
?
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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
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
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-
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
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-
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LL-2,6-Diaminoheptanedioate
?
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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
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-
-
LL-2,6-Diaminoheptanedioate
?
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enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
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LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Q8NP73
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-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Q8NP73
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-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
E4NI20
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-
-
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
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stereo-conversion, the product complex (Enzyme/meso-diaminopimelate) is less stable than the reactant complex (Enzyme/LL-diaminopimelate)
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r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
-
stereo-inversion
the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
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?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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the enzyme is independent of pyridoxal 5'-phosphate
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additional information
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the enzyme is independent of pyridoxal 5'-phosphate
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-(4-amino-4-carboxybutyl)-aziridine-2-carboxylate
substrate mimic, irreversible inhibition
3-Chlorodiaminopimelate
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the inhibitor is converted to a tight-binding transition state analog at the active site of this enzyme
4-Oxo-1,2,3,4-tetrahydro-pyridine-2,6-dicarboxylic acid
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very poor inhibitor
dilithium (2Z,6S)-2,6-diamino-4-oxohept-2-enedioate
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competitive, IC50: 0.5 mM
DL-aziridino analogues of diaminoheptanedioate
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DL-aziridino diaminopimelic acid, irreversible inhibitor
DL-aziridino-diaminopimelate
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product-like inhibitor, inhibitor mimics the natural substrate, the methylene carbon of the aziridine ring of the 2 diastereomeric inhibitors is covalently bonded to the sulfur atom of Cys73 or Cys217 after the nucleophilic attack of the sulfur on the aziridine ring that irreversibly inhibits the enzyme
LL-aziridino analogues of diaminoheptanedioate
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LL-aziridino diaminopimelic acid, irreversible inhibitor
LL-aziridino-diaminopimelate
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reactant-like inhibitor, inhibitor mimics the natural substrate, the methylene carbon of the aziridine ring of the 2 diastereomeric inhibitors is covalently bonded to the sulfur atom of Cys73 or Cys217 after the nucleophilic attack of the sulfur on the aziridine ring that irreversibly inhibits the enzyme
iodoacetamide
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half-life for inactivation with 0.25 mM iodoacetamide is 9.6 min
additional information
-
none of the following compounds shows significant inhibition: (2S)-2-amino-3-(4-carboxyimidazol-1-yl)propanoic acid, (2S,5'R)-2-amino-3-(3-carboxy-2-isoxazolin-5-yl)propanoic acid and its 5'S diastereomer, 2-isoxazoline-3-carboxylic acid, and 2-isoxazoline-3,5-dicarboxylic acid
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
thiol compound
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2,3-dimercaptopropan-1-ol is most effective; required for activity
additional information
-
no pyridoxal phosphate requirement; one, but not both, of the proton acceptor sites is a thiol
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
12 - 17
meso-diaminoheptanedioate
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recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.5
dilithium (2Z,6S)-2,6-diamino-4-oxohept-2-enedioate
Escherichia coli
-
competitive, IC50: 0.5 mM
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
1.61
purified recombinant His-tagged enzyme, substrate meso-diaminoheptanedioate, pH 6.8, 30°C
4.93
purified recombinant His-tagged enzyme, substrate LL-2,6-diaminoheptanedioate, pH 6.8, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 8
7.5
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maximum activity of recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8.5
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pH 6: about 60% of maximal activity, pH 8.5: about 25% of maximal activity
6.5 - 9
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recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
45
-
the relative rates of epimerization of LL-diaminoheptanedioate at 25°C, 37°C and 45°C are 0.77:1.00:1.15
30
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recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame is almost 50% more active at 30°C than at 25°C
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 45
-
the relative rates of epimerization of LL-diaminoheptanedioate at 25°C, 37°C and 45°C are 0.77:1.00:1.15
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
natural excretor of lysine, lysine-overproducing homoserine auxotroph strain and its auxotrophic and multi-analogue-resistant high-yielding mutant AEC NV 20r50
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brenda
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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UniProt
brenda
-
-
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
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
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meso-diaminopimelate is a biosynthetic precursor of L-lysine in bacteria
metabolism
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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
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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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
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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
-
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
-
(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
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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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
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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
-
the structure of Chlamydia DAP epimerase exhibits significant remodeling in the substrate-binding pocket, overview
additional information
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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C83 and C221 are catalytic residues
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Escherichia coli (strain K12)
Escherichia coli O45:K1 (strain S88 / ExPEC)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Escherichia coli O45:K1 (strain S88 / ExPEC)
Escherichia coli O45:K1 (strain S88 / ExPEC)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30000
-
molecular weight of recombinant DapF consisting of silent mutation of the first 10 codons, determined by SDS-PAGE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
-
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
dimer
CgDapF functions as a dimer and the asymmetric unit contains a CgDapF dimer, the dimerization interface is mainly constituted by the contacts between beta16 from both monomers, and contact between two beta-strands connects the two beta-sheets of the N-terminal domains (NTDs) from both monomers. Contacts between the connecting loops (alpha1-beta3) from both monomers also mediate dimerization of the protein. Each CgDapF monomer consists of two distinct domains: an NTD (Met1-Asp131 and Gly268-Ile277) and a C-terminal domain (CTD, Met132-Thr267). Each domain contains a set of five-stranded and three-stranded antiparallel beta-sheets and two alpha-helices. One alpha-helix of each domain (alpha2 in the NTD and alpha4 in the CTD) is sandwiched between the five-stranded and three-stranded beta-sheets, whereas the other helix lies on the surface of the protein. The NTD and the CTD are structurally homologous to each other, structure comparisons of DAP epimerases, overview
dimer
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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CgDapF functions as a dimer and the asymmetric unit contains a CgDapF dimer, the dimerization interface is mainly constituted by the contacts between beta16 from both monomers, and contact between two beta-strands connects the two beta-sheets of the N-terminal domains (NTDs) from both monomers. Contacts between the connecting loops (alpha1-beta3) from both monomers also mediate dimerization of the protein. Each CgDapF monomer consists of two distinct domains: an NTD (Met1-Asp131 and Gly268-Ile277) and a C-terminal domain (CTD, Met132-Thr267). Each domain contains a set of five-stranded and three-stranded antiparallel beta-sheets and two alpha-helices. One alpha-helix of each domain (alpha2 in the NTD and alpha4 in the CTD) is sandwiched between the five-stranded and three-stranded beta-sheets, whereas the other helix lies on the surface of the protein. The NTD and the CTD are structurally homologous to each other, structure comparisons of DAP epimerases, overview
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
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
-
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); 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 substrates’nonacidic hydrogen at the alpha-carbon by a seemingly weakly basic cysteine residue is facilitated by interactions with two buried alpha-helices
-
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 thiol–thiolate 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; 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
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
N159A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, nearly inactive mutant
-
N74A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, nearly inactive mutant
-
N85A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, nearly inactive mutant
-
R213A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, nearly inactive mutant
-
T223A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
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
C73S/C217S
C87S
-
severely compromised catalytic efficiency despite decrease in Km value
C87S
-
severely compromised catalytic efficiency despite decrease in Km value
-
additional information
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
-
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5
-
2°C, overnight, 0.1 mM 2,3-dimercaptopropan-1-ol, 20% loss of activity
2136
6
-
irreversible loss of activity at pH 6 and below. Partially reactivated by thiols
2140
8.5
-
2°C, overnight, 0.1 mM 2,3-dimercaptopropan-1-ol, 70% loss of activity
2136
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
air oxidation, in absence of reducing thiols, is slower at pH 7 than at pH 8
-
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Acetone
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
by immobilized nickel metal-affinity chromatography using 5 ml HisTrap HP columns and by gel filtration as His-tagged enzyme
-
protein is applied to a Ni21-primed chelating sepharose column, and DapF-containing eluate, fractions are dialysed and further purified by anion exchange chromatography on a HiTrap Q Sepharose FF column, representing a yield of 1 mg/L culture
-
recombinant His6-tagged enzyme from Escherichia coli strain SoluBL21 by nickel affinity chromatography, tag cleavage by thrombin, another step of nickel affinity chromatography, ultrafiltration, and gel filtration
-
recombinant N-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS/pET15b by nickel affinity chromatography
recombinant seleno-methionine substituted wild-type and mutant enzymes from Escherichia coli strain B834(DE3)
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
DAP epimerase mutants C73S and C217S from Haemophilus influenzae are cloned and purified
-
gene dapF, overexpression of N-terminally His6-tagged enzyme, cloned with a a thrombin cleavage site, in Escherichia coli strain SoluBL21
-
gene dapF, recombinant expression of seleno-methionine substituted wild-type and mutant enzymes in Escherichia coli strain B834(DE3)
gene dapF, sequence comparisons and phylogenetic analysis, Chlamydia trachomatis dapF restores growth in an Escherichia coli D-glutamate auxotroph strain WM335 also lacking endogenaous gene dapF, expression under the control of an arabinose-inducible promoter, the recombinant enzyme is capable of both DAP epimerase and D-glut racemase activities, DapFCT is also capable of racemizing D-Glu to L-Glu
-
gene dapF1, expression of N-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS/pET15b
recombinant protein is expressed as His-tegged enzyme in BL21(DE3) Escherichia coli cells
-
since previous attempts to express the diaminopimelate epimerase gene dapF of Mycobacterium tuberculosis in Escherichia coli results in undetectable enzyme yields a recombinant DapF protein is expressed in Escherichia coli consisting of silent mutation of the first 10 codons of the open reading frame in an attempt to reduce the formation of secondary structures that occur near the 5' end of the mRNA and inhibit translation. This significantly increases the yield of the enzyme
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
drug development
analysis
-
simple and sensitive spectrophotometric method for the determination of meso-alpha,epsilon-diaminopimelate with meso-2,6-diaminopimelate D-dehydrogenase and its application to the assay of diaminopimelate epimerase
analysis
-
a high-performance liquid chromatography method for the simultaneous assay of diaminopimelate epimerase and decarboxylase
drug development
-
diaminopimelate epimerase catalyzes the stereoinversion of LL-diaminopimelate to meso-diaminopimelate, a precursor of L-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials
drug development
-
the recombinant DapF produced is correctly folded and is a suitable tool for a drug development study
drug development
-
bacterial racemase, including glutamate racemase and DAP epimerase, are potential targets for the development of new agents effective against organisms resistant to conventional antibiotics
drug development
-
DAP epimerase is an attractive target for rational antibiotic design
drug development
-
enzyme represents a promising target for rational drug design aimed to develop new selective antibacterial therapeutic agents
drug development
the enzme is an attractive target to facilitate development of antibacterial agents
drug development
DapF is considered as an attractive target for the development of antibacterial drugs
drug development
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
DapF is considered as an attractive target for the development of antibacterial drugs
-
drug development
-
the enzme is an attractive target to facilitate development of antibacterial agents
-
drug development
-
the recombinant DapF produced is correctly folded and is a suitable tool for a drug development study
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Adams, E.
Amino acid racemases and epimerases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
6
479-507
1972
Bacillus megaterium, Escherichia coli
-
brenda
Withe, P.J.; Lejeune, B.; Work, E.
Assay and properties of diaminopimelate epimerase from Bacillus megaterium
Biochem. J.
113
589-601
1969
Bacillus 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
Bacillus circulans, Bacillus megaterium, Brevibacillus laterosporus, Geobacillus stearothermophilus, no activity in Bacillus globisporus, no activity in Bacillus pasteurii, no activity in Bacillus sphaericus, Paenibacillus macerans, Paenibacillus polymyxa, 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
Bacillus 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, Haemophilus influenzae (P44859)
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, Haemophilus influenzae (P44859)
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, Mycobacterium tuberculosis (P9WP19), 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, Arabidopsis thaliana (Q9LFG2)
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, Mycobacterium tuberculosis (P9WP19), 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.; Altoè, 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, Corynebacterium glutamicum (Q8NP73), Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 (Q8NP73)
brenda
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