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(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-2,6-Diaminoheptanedioate
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
LL-3-fluoro-2,6-diaminopimelic acid
tetrahydrodipicolinic acid + HF
-
slow elimination of HF
-
?
LL-oxa-diaminopimelic acid
meso-oxa-diaminopimelic acid
-
-
-
-
?
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
additional information
?
-
LL-2,6-Diaminoheptanedioate

?
-
enzyme of Lys biosynthesis
-
-
-
LL-2,6-Diaminoheptanedioate
?
-
enzyme of Lys biosynthesis
-
-
-
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
-
-
-
LL-2,6-Diaminoheptanedioate
?
-
enzyme of the diaminopimelic acid pathway for biosynthesis of Lys
-
-
-
LL-2,6-Diaminoheptanedioate

meso-Diaminoheptanedioate
-
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
r, between 25°C and 45°C at pH 7.0, the equilibrium mixture contains 65% meso-isomer and 35% LL-isomer
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
Chlamydomonas sp.
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
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-Diaminoheptanedioate
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
r
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
?
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-Diaminoheptanedioate
meso-Diaminoheptanedioate
-
-
-
-
LL-2,6-diaminoheptanedioate

meso-diaminopimelate
-
stereo-inversion
-
-
?
LL-2,6-diaminoheptanedioate
meso-diaminopimelate
-
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
-
stereo-inversion
the meso-isomer of diaminopimelic acid, a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan
-
?
meso-diaminoheptanedioate

LL-2,6-diaminoheptanedioate
-
-
-
r
meso-diaminoheptanedioate
LL-2,6-diaminoheptanedioate
-
-
-
r
additional information

?
-
-
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
?
-
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
?
-
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
-
-
-
additional information
?
-
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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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.; Altoč, 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