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Information on EC 5.1.1.7 - diaminopimelate epimerase
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EC Tree
5.1.1.7 diaminopimelate epimeraseSpecify your search results
Word Map
- 5.1.1.7
-
meso-dap
- racemase
- peptidoglycan
- l-lysine
- drug development
-
ll-dap
-
plp-independent
- meso-diaminopimelate
-
epimerization
- d-cycloserine
-
stereoinversion
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l,l-diaminopimelate
-
two-base
- analysis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
diaminopimelate epimerase, dap epimerase, diaminopimelic acid epimerase, mtdapf, cgdapf, dapfct, 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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-
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Epimerase, diaminopimelate
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-
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LL-Diaminopimelate epimerase
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-
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MtDapF
DAP epimerase
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-
-
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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 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
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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
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rapid elimination, enamine product is formed which spontaneously cyclizes to tetrahydrodipicolinic acid
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?
LL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
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slow elimination of HF
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?
LL-oxa-diaminopimelic acid
meso-oxa-diaminopimelic acid
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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
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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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-
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r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
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-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
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-
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r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
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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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-
-
?
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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?
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
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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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?
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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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-
?
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
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-
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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
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r
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
-
?
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
-
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-carboxylic acid)
AziDAP
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
5,5'-dithiobis(2-nitrobenzoic acid)
30 nM, complete inhibition
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
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
iodoacetamide
-
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
additional information
-
one, but not both, of the proton acceptor sites is a thiol
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Tuberculosis
Characterization of Mycobacterium tuberculosis diaminopimelic acid epimerase: paired cysteine residues are crucial for racemization.
Tuberculosis
Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis.
Tuberculosis
Use of a codon alteration strategy in a novel approach to cloning the Mycobacterium tuberculosis diaminopimelic acid epimerase.
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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
0.0025
meso-diaminoheptanedioate
mutant C226S, pH 7.5, 30°C
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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
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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
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the relative rates of epimerization of LL-diaminoheptanedioate at 25°C, 37°C and 45°C are 0.77:1.00:1.15
30
-
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