Information on EC 5.1.1.7 - diaminopimelate epimerase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY
5.1.1.7
-
RECOMMENDED NAME
GeneOntology No.
diaminopimelate epimerase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
show the reaction diagram
two-base mechanism for proton translocation. One, but not both, of the proton acceptor sites is a thiol
-
-
-
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
show the reaction diagram
molecular dynamics simulations show that the configuration of the distal carbon C6 of L,L-DAP is critical for complex formation since both amino and carboxylate groups are involved in Hbonding interactions with the active site residues. Furthermore, the interactions occurring between the functional groups bonded to the C2 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
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
epimerization
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
L-lysine biosynthesis I
-
-
L-lysine biosynthesis II
-
-
L-lysine biosynthesis VI
-
-
Lysine biosynthesis
-
-
lysine metabolism
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
LL-2,6-diaminoheptanedioate 2-epimerase
-
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
DAP epimerase
-
-
-
-
DAP-epimerase
-
-
-
-
Diaminopimelic acid epimerase
-
-
-
-
Diaminopimelic epimerase
-
-
-
-
Epimerase, diaminopimelate
-
-
-
-
LL-Diaminopimelate epimerase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9024-22-0
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
natural excretor of lysine, lysine-overproducing homoserine auxotroph strain and its auxotrophic and multi-analogue-resistant high-yielding mutant AEC NV 20r50
-
-
Manually annotated by BRENDA team
Chlamydomonas sp.
-
-
-
Manually annotated by BRENDA team
gene dapF
-
-
Manually annotated by BRENDA team
gene dapF1; gene dapF1
UniProt
Manually annotated by BRENDA team
Kitasatospora setae KM-6054T
gene dapF1; gene dapF1
UniProt
Manually annotated by BRENDA team
no activity in Bacillus globisporus
-
-
-
Manually annotated by BRENDA team
no activity in Bacillus pasteurii
-
-
-
Manually annotated by BRENDA team
no activity in Bacillus sphaericus
-
-
-
Manually annotated by BRENDA team
Mixed rumen bacteria
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
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
E4NI20
diaminopimelate isomers are not only intermediates of the lysine biosynthesis diaminopimelate pathway but also essential components of bacterial peptidoglycan
physiological function
Kitasatospora setae KM-6054T
-
diaminopimelate isomers are not only intermediates of the lysine biosynthesis diaminopimelate pathway but also essential components of bacterial peptidoglycan
-
metabolism
-
meso-diaminopimelate is a biosynthetic precursor of L-lysine in bacteria
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
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S,6S)-2,6-diaminoheptanedioate
meso-diaminoheptanedioate
show the reaction diagram
-
-
-
?
DL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
show the reaction diagram
-
rapid elimination, enamine product is formed which spontaneously cyclizes to tetrahydrodipicolinic acid
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
P44859
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
Chlamydomonas sp.
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
E4NI20
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
r, between 25C and 45C at pH 7.0, the equilibrium mixture contains 65% meso-isomer and 35% LL-isomer
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
Kitasatospora setae KM-6054T
E4NI20
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
Bacillus megaterium CII 19
-
-
-
-
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
-
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
-
-
-
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
-
enzyme of Lys biosynthesis
-
-
-
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
-
enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
-
-
-
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
Bacillus megaterium CII 19
-
enzyme of Lys biosynthesis
-
-
-
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
show the reaction diagram
-
stereo-conversion, the product complex (Enzyme/meso-diaminopimelate) is less stable than the reactant complex (Enzyme/LL-diaminopimelate)
-
-
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
show the reaction diagram
-
stereo-inversion
-
-
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
show the reaction diagram
-
stereo-inversion
the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
-
?
LL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
show the reaction diagram
-
slow elimination of HF
-
?
LL-oxa-diaminopimelic acid
meso-oxa-diaminopimelic acid
show the reaction diagram
-
-
-
-
?
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
show the reaction diagram
P9WP19
-
-
-
r
additional information
?
-
Q9LFG2
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
-
-
-
additional information
?
-
Kitasatospora setae, Kitasatospora setae KM-6054T
E4NI20
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
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
-
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
show the reaction diagram
E4NI20
-
-
-
r
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
-
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
-
-
-
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
-
enzyme of Lys biosynthesis
-
-
-
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
-
enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
-
-
-
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
show the reaction diagram
-
stereo-conversion, the product complex (Enzyme/meso-diaminopimelate) is less stable than the reactant complex (Enzyme/LL-diaminopimelate)
-
-
r
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
show the reaction diagram
-
stereo-inversion
-
-
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
show the reaction diagram
-
stereo-inversion
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-Diaminoheptanedioate
show the reaction diagram
Kitasatospora setae KM-6054T
E4NI20
-
-
-
r
LL-2,6-Diaminoheptanedioate
?
show the reaction diagram
Bacillus megaterium CII 19
-
enzyme of Lys biosynthesis
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
the enzyme is independent of pyridoxal 5'-phosphate
-
additional information
-
the enzyme is independent of pyridoxal 5'-phosphate
-
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(2-(4-amino-4-carboxybutyl) aziridine-2-carboxylic acid)
-
AziDAP
1,2-benzisothiazolidine 3-one
-
30 nM, complete inhibition
2-(4-amino-4-carboxybutyl)-aziridine-2-carboxylate
Q9LFG2
substrate mimic, irreversible inhibition
2-(4-amino-4-carboxybutyl)aziridine-2-carboxylic acid
-
irreversible
2-nitro-5-thiocyanatobenzoate
-
30 nM, complete inhibition
3-Chlorodiaminopimelate
-
the inhibitor is converted to a tight-binding transition state analog at the active site of this enzyme
3-Fluoro analogs of diaminopimelate
-
potent competitive inhibitors
-
4-Oxo-1,2,3,4-tetrahydro-pyridine-2,6-dicarboxylic acid
-
very poor inhibitor
5,5'-dithiobis(2-nitrobenzoic acid)
-
30 nM, complete inhibition
acetone
E4NI20
inactivation by 50% acetone
dilithium (2Z,6S)-2,6-diamino-4-oxohept-2-enedioate
-
competitive, IC50: 0.5 mM
DL-aziridino analogues of diaminoheptanedioate
-
DL-aziridino diaminopimelic acid, irreversible inhibitor
DL-aziridino-diaminopimelate
-
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
hydroxylamine
-
no inhibition
hydroxylamine
-
; no inhibition
iodoacetamide
-
half-life for inactivation with 0.25 mM iodoacetamide is 9.6 min
iodoacetamide
-
-
Isoniazid
-
-
Lanthionine isomers
-
-
-
Lanthionine sulfone
-
-
Lanthionine sulfoxide
-
-
LL-aziridino analogues of diaminoheptanedioate
-
LL-aziridino diaminopimelic acid, irreversible inhibitor
LL-aziridino-diaminopimelate
-
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
N-Aminodiaminopimelate
-
-
N-Hydroxydiaminopimelate
-
-
Phosphonate analogs of diaminopimelate
-
-
-
Semicarbazide
-
no inhibition
Semicarbazide
-
-
Mercurials
-
-
-
additional information
-
no inhibition by deoxypyridioxine
-
additional information
-
-
-
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
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
thiol compound
-
2,3-dimercaptopropan-1-ol is most effective; required for activity
thiol compound
-
required for activity
additional information
-
no pyridoxal phosphate requirement
-
additional information
-
pyridoxal phosphate does not stimulate
-
additional information
-
no pyridoxal phosphate requirement; one, but not both, of the proton acceptor sites is a thiol
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.16
LL-diaminoheptanedioate
-
-
6.7
LL-diaminoheptanedioate
-
at 37C
0.07
meso-diaminoheptanedioate
-
mutant C87S, pH 7.5, 30C
0.166
meso-diaminoheptanedioate
-
wild-type, pH 7.5, 30C
0.215
meso-diaminoheptanedioate
-
mutant C226S, pH 7.5, 30C
0.36
meso-diaminoheptanedioate
-
-
0.36
meso-diaminoheptanedioate
-
LL-diaminoheptanedioate
12 - 17
meso-diaminoheptanedioate
-
recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame
100
meso-diaminoheptanedioate
-
at 37C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
128
LL-2,6-Diaminoheptanedioate
-
forward reaction
84
LL-diaminoheptanedioate
-
-
0.001
meso-diaminoheptanedioate
-
mutant C87S, pH 7.5, 30C
0.0025
meso-diaminoheptanedioate
-
mutant C226S, pH 7.5, 30C
0.1465
meso-diaminoheptanedioate
-
wild-type, pH 7.5, 30C
67
meso-diaminoheptanedioate
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.5
dilithium (2Z,6S)-2,6-diamino-4-oxohept-2-enedioate
-
competitive, IC50: 0.5 mM
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.205
-
crude extract after expression
0.574
-
after immobilized metal-affinity chromatography
1.18
-
after gel filtration
1.61
E4NI20
purified recombinant His-tagged enzyme, substrate meso-diaminoheptanedioate, pH 6.8, 30C
4.93
E4NI20
purified recombinant His-tagged enzyme, substrate LL-2,6-diaminoheptanedioate, pH 6.8, 30C
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 8
-
in both directions
6.8
E4NI20
assay at
7.5
-
maximum activity of recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8.5
-
pH 6: about 60% of maximal activity, pH 8.5: about 25% of maximal activity
6.5 - 9
-
recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
-
recombinant DapF consisting of silent mutation of the first 10 codons of the open reading frame is almost 50% more active at 30C than at 25C
30
E4NI20
assay at
45
-
the relative rates of epimerization of LL-diaminoheptanedioate at 25C, 37C and 45C are 0.77:1.00:1.15
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 45
-
the relative rates of epimerization of LL-diaminoheptanedioate at 25C, 37C and 45C are 0.77:1.00:1.15
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
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)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
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
673738
31030
-
predicted, confirmed by SDS-PAGE
701554
45400
-
gel filtration
2140
61300
-
recombinant enzyme, analytical ultracentrifugation
727975
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
-
2 * 31031, recombinant enzyme, mass spectrometry
monomer
-
1 * 34000, SDS-PAGE
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
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
Q9LFG2
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, 20C, 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 substratesnonacidic 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 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; 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
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5
-
2C, 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
-
rapid loss of activity when stored in absence of dithiothreitol
2155
8.5
-
2C, overnight, 0.1 mM 2,3-dimercaptopropan-1-ol, 70% loss of activity
2136
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
air oxidation, in absence of reducing thiols, is slower at pH 7 than at pH 8
-
denatured on freezing
-
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Acetone
E4NI20
inactivation by 50% acetone
Acetone
Kitasatospora setae KM-6054T
-
inactivation by 50% acetone
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0-4C, best storage temperature
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
-
by immobilized nickel metal-affinity chromatography using 5 ml HisTrap HP columns and by gel filtration as His-tagged enzyme
-
recombinant N-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS/pET15b by nickel affinity chromatography
E4NI20
by using nickel-chelate affinity chromatography
-
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
-
partial
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene dapF, overexpression of N-terminally His6-tagged enzyme, cloned with a a thrombin cleavage site, in Escherichia coli strain SoluBL21
-
expressed in Escherichia coli BL21 (DE3)
-
DAP epimerase mutants C73S and C217S from Haemophilus influenzae are cloned and purified
-
expression in Escherichia coli BL21(DE3)
-
gene dapF1, expression of N-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS/pET15b
E4NI20
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
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
-
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
C226A
-
complete loss of activity
C226S
-
severely compromised catalytic efficiency
C87A
-
complete loss of activity
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
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
C87S
-
severely compromised catalytic efficiency despite decrease in Km value
-
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
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
a high-performance liquid chromatography method for the simultaneous assay of diaminopimelate epimerase and decarboxylase
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
drug development
-
DAP epimerase is an attractive target for rational antibiotic design
drug development
-
the enzyme is a promising antimicrobial target
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
-
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
-
enzyme represents a promising target for rational drug design aimed to develop new selective antibacterial therapeutic agents
drug development
E4NI20
the enzme is an attractive target to facilitate development of antibacterial agents
drug development
Kitasatospora setae KM-6054T
-
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
drug development
-
the recombinant DapF produced is correctly folded and is a suitable tool for a drug development study
-