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evolution

-
the enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family
evolution
the enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family
metabolism

-
DapE is involved in the meso-diaminopimelate (mDAP)/lysine biosynthetic pathway
metabolism
DapE is involved in the meso-diaminopimelate, mDAP/lysine biosynthetic pathway
metabolism
the enzyme catalyzes the seventh reaction step of the succinyl pathway
metabolism
-
the enzyme is part of the lysine biosynthetic pathway which is indispensable for bacterial survival
physiological function

-
DapE is a critical bacterial enzyme for the construction of the bacterial cell wall.
physiological function
DapE is essential for cell growth and proliferation
additional information

-
residues Arg178, Thr325, and Asn345 play a role in substrate identification and stabilization of the enzyme active site. The glycine rich loop, Gly322-Ser326, facilitates tight binding of the substrate in the enzyme active site. Computational structure modeling by quantum mechanics/molecular mechanics calculations using the enzyme crystal structure PDB ID 3IC1
additional information
-
structural comparisons of wild-type and inactive monomeric DapE enzymes with other M20 peptidases, active site and zinc binding structure, molecular modeling and dynamics simulations, overview. The dimerization domain in DapE enzymes is required for catalysis. Removal of the dimerization domain increases the flexibility of a conserved active site loop that may provide critical interactions with the substrate
additional information
structural comparisons of wild-type and inactive monomeric DapE enzymes with other M20 peptidases, active site and zinc binding structure, molecular modeling and dynamics simulations, overview. The dimerization domain in DapE enzymes is required for catalysis. Removal of the dimerization domain increases the flexibility of a conserved active site loop that may provide critical interactions with the substrate
additional information
-
structural comparisons of wild-type and inactive monomeric DapE enzymes with other M20 peptidases, active site and zinc binding structure, molecular modeling and dynamics simulations, overview. The dimerization domain in DapE enzymes is required for catalysis. Removal of the dimerization domain increases the flexibility of a conserved active site loop that may provide critical interactions with the substrate
additional information
-
DapE residues H355 and H80 are active site ligands, divalent metal binding properties of co-catalytic metallohydrolase active site, overview. Three-dimensional homological structure molecular modeling of N-acetyl-L-ornithine deacetylase, EC 3.5.1.16, from Escherichia coli, using the X-ray crystal structure of the DapE from Haemophilus influenzae, PDB ID 3IC1, as template
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(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
?
-
high stereospecificity
-
?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
N-succinyl-DL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
N-succinyl-LL-2,6-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-diaminopimelate + H2O
?
-
-
-
-
?
N-succinyl-LL-diaminopimelic acid + H2O
?
-
-
-
-
?
additional information
?
-
N-succinyl LL-diaminopimelic acid + H2O

succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
N-succinyl-DL-2,6-diaminoheptanedioate + H2O

succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-DL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O

succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
i.e. N-succinyl-L,L-diaminopimelic acid
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
?
additional information

?
-
-
acetylornithine deacetylase, succinyldiaminopimelate desuccinylase and carboxypeptidase G2 are evolutionarily related
-
-
-
additional information
?
-
-
kinetic mechanism
-
-
-
additional information
?
-
-
structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
-
-
-
additional information
?
-
-
kinetic mechanism
-
-
-
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N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
additional information
?
-
N-succinyl LL-diaminopimelic acid + H2O

succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
P44514
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O

succinate + LL-2,6-diaminoheptanedioate
Q59284
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Q59284
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
P9WHS9
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
i.e. N-succinyl-L,L-diaminopimelic acid
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Q9KQ52
-
-
-
?
additional information

?
-
-
acetylornithine deacetylase, succinyldiaminopimelate desuccinylase and carboxypeptidase G2 are evolutionarily related
-
-
-
additional information
?
-
-
kinetic mechanism
-
-
-
additional information
?
-
-
structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
-
-
-
additional information
?
-
-
kinetic mechanism
-
-
-
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Cd2+
-
65% of activity with Zn2+
sulfate
in one of the monomers of the ZnZn_DapE structure, both of these residues form a charged dipole interaction with a sulfate ion, a possible mimic of the carboxylic group of the substrate
Co2+

-
required and most active as a cofactor
Co2+
-
125% of activity with Zn2+
Co2+
-
can substitute for Zn2+
Mn2+

-
required
Mn2+
-
20% of activity with Zn2+
Zn2+

-
required
Zn2+
-
the enzyme requires two Zn2+ ions. Each of the Zn(II) ions adopts a distorted tetrahedral geometry and is coordinated by one imidazole group, H67 for Zn1 and H349 for Zn2, and one carboxylate group, E163 for Zn1 and E135 for Zn2. Both Zn(II) ions are bridged by an additional carboxylate groups of residue D100 on one side and water/hydroxide on the opposite side, forming a (mu-aquo)(mu-carboxylato)dizinc(II) core with one terminal carboxylate and one histidine residue at each metal site
Zn2+
-
modelling of binding structure, overview
Zn2+
required for activity, DapE has one or two zinc ions bound in the active site, the two forms show different activity, structures of monometalated and dimetalated forms, overview
Zn2+
-
di-nuclear Zn2+ enzyme, the side chain of Asp100 bridges the two Zn centers of the enzyme
Zn2+
-
required, dinuclear Zn(II)-loaded enzyme, binding structure, overview
Zn2+
-
required, the enzyme binds two Zn(II) ions in non-interactive binding sites with Kd values for the first Zn(II) binding event of 0.0044 mM, whereas the observed Kd values for the second metal binding event in DapE is 0.0136 mM
Zn2+
-
the enzyme possesses a catalytic domain with a di-zinc active site
Zn2+
required, dinuclear Zn(II)-loaded enzyme, binding structure, overview
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0.26 - 0.99
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
730
N-succinyl LL-diaminopimelic acid
pH not specified in the publication, temperature not specified in the publication
3.2
N-succinyl-DL-2,6-diaminoheptanedioate
-
in the presence of Zn2+
0.8 - 4.7
N-succinyl-LL-2,6-diaminoheptanedioate
0.73 - 1.4
N-succinyl-LL-2,6-diaminopimelic acid
-
0.65 - 0.73
N-succinyl-LL-diaminopimelate
0.26
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid

-
pH 7.5, 30°C, ZnCo-loaded enzyme
0.73
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30°C, Zn-loaded enzyme; pH 7.5, 30°C, ZnZn-loaded enzyme
0.74
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30°C, CoZn-loaded enzyme
0.99
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30°C, CoCo-loaded enzyme; pH 7.5, 30°C, Co-loaded enzyme
0.8
N-succinyl-LL-2,6-diaminoheptanedioate

-
pH 7.5, 25°C, recombinant wild-type enzyme
1.2
N-succinyl-LL-2,6-diaminoheptanedioate
pH 7.5, 25°C, recombinant enzyme
1.3
N-succinyl-LL-2,6-diaminoheptanedioate
-
37°C, pH 8.1
1.3
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Zn2+
1.5
N-succinyl-LL-2,6-diaminoheptanedioate
-
37°C, pH 8.1, in the presence of Co2+
1.6
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Co2+
2.1
N-succinyl-LL-2,6-diaminoheptanedioate
-
pH 7.5, 25°C, recombinant mutant T325A
3
N-succinyl-LL-2,6-diaminoheptanedioate
-
pH 7.5, 25°C, recombinant mutant T325S
4.7
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Co2+
0.73
N-succinyl-LL-2,6-diaminopimelic acid

-
pH 7.5, 30°C, wild-type enzyme
-
1.4
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30°C, mutant H67A
-
0.65
N-succinyl-LL-diaminopimelate

-
mutant enzyme E134D at pH 7.5
0.73
N-succinyl-LL-diaminopimelate
-
wild type enzyme at pH 7.5
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140
N-succinyl LL-diaminopimelic acid
pH not specified in the publication, temperature not specified in the publication
0.0555 - 114
N-succinyl-LL-2,6-diaminoheptanedioate
1.5 - 140
N-succinyl-LL-2,6-diaminopimelic acid
-
0.13 - 140
N-succinyl-LL-diaminopimelate
0.0555
N-succinyl-LL-2,6-diaminoheptanedioate

-
in the presence of zinc
2.9
N-succinyl-LL-2,6-diaminoheptanedioate
-
pH 7.5, 25°C, recombinant mutant T325S
4
N-succinyl-LL-2,6-diaminoheptanedioate
-
pH 7.5, 25°C, recombinant mutant T325A
80
N-succinyl-LL-2,6-diaminoheptanedioate
pH 7.5, 25°C, recombinant enzyme
114
N-succinyl-LL-2,6-diaminoheptanedioate
-
pH 7.5, 25°C, recombinant enzyme
1.5
N-succinyl-LL-2,6-diaminopimelic acid

-
pH 7.5, 30°C, mutant H67A
-
140
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30°C, wild-type enzyme
-
0.13
N-succinyl-LL-diaminopimelate

-
mutant enzyme E134D at pH 7.5
140
N-succinyl-LL-diaminopimelate
-
wild type enzyme at pH 7.5
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1.62
(2-carboxyethyl)-phosphonic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
17
2-amino-6-[(2-methylpropanoyl)amino]heptanedioic acid
Haemophilus influenzae
-
pH 7.5, 25°C
0.092
2-thiopheneboronic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
0.034
3-mercaptobenzoic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
0.043
4-sulfanylbutanoic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
1
aceto-hydroxamic acid
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.042
D-captopril
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
-
0.05
D-penicillamine
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
1
enalapril
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.0137
L-Penicillamine
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
1
N-(benzyloxycarbonyl)hydroxylamine
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.01
N-phenyl-thiourea
Haemophilus influenzae
-
above, pH not specified in the publication, temperature not specified in the publication
0.107
phenylboronic acid
Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
0.0033
L-captopril

Haemophilus influenzae
-
pH not specified in the publication, temperature not specified in the publication
0.0033
L-captopril
Salmonella enterica
-
pH and temperature not specified in the publication
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sitting nanodroplet vapor diffusion method, using 6 mM ZnCl2, 43.1% (w/v) polyethylene glycol 400, 0.2 M sodium chloride, 0.1 M sodium/potassium phosphate pH 6.4, at 20°C
crystal structure, PDB ID 3IC1, analysis, comparison with the structure of N-acetyl-L-ornithine deacetylase, EC 3.5.1.16, overview
-
purified recombinant wild-type and mutant G172D enzymes, apoform and Zn2+-bound enzyme, using 400 nl of a precipitant solution containing 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG 3350, and 400 nl of 15 mg/ml of protein in crystallization buffer, with or without 1 mM ZnCl2, within 14 days, X-ray diffraction structure determination and analysis at 1.84 A resolution
-
ultrapure recombinant DapE with one and two zinc ions bound in the active site, respectively, at 16°C, by vapor diffusion in hanging drops containing 1 ml of precipitant solution containing 1 M ammonium sulfate, 0.2 M NaCl, and 0.1 M Na acetate, pH 4.4, and 0.001 ml of 13 mg/ml of DapE with three equivalents of zinc, 2 weeks, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, 0.001-0.002 ml of 3-7 mg/ml protein in 50 mM Bis-Tris, pH 6.0, 200 mM NaCl, 0.5 mM TCEP is mixed with 0.001-0.002 ml reservoir solution, containing 5-10% w/v PEG 4000 or PEG 3350, 35-120 mM ammonium sulfate, 100 mM sodium acetate, pH 4.1-4.6, and equilibrated against 0.9 ml reservoir solution, at room temperature, 1 day, method optimization, X-ray diffraction structure determination and analysis at 2.4-2.58 A resolution, two crystal forms
purified recombinant enzyme, apoform and Zn2+-bound enzyme, using 400 nl of a precipitant solution containing 20% v/v 1,4-butanediol, 0.1 M sodium acetate, pH 4.5, and 400 nl of 19 mg/ml protein in crystallization buffer, with or without 1 mM ZnCl2, within 14 days, X-ray diffraction structure determination and analysis at 1.65 A resolution
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Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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Boyen, A.; Charlier, D.; Charlier, J.; Sakanyan, V.; Mett, I.; Glansdorff, N.
Acetylornithine deacetylase, succinyldiaminopimelate desuccinylase and carboxypeptidase G2 are evolutionarily related
Gene
116
1-6
1992
Escherichia coli
brenda
Kindler, S.H.; Gilvarg, C.
N-succinyl-L-alpha, epsilon-diaminopimelic acid deacylase
J. Biol. Chem.
235
3552-3535
1960
Alcaligenes faecalis, Azotobacter vinelandii, Bacillus cereus, Bacillus cereus No.48292, Corynebacterium diphtheriae, Corynebacterium diphtheriae P.W.8, Escherichia coli, Escherichia coli M-26-26, Micrococcus luteus, Rhodobacter sphaeroides
-
brenda
Born, T.L.; Zheng, R.; Blanchard, J.S.
Hydrolysis of N-succinyl-L,L-diaminopimelic acid by Haemophilus influenzae dapE-encoded desuccinylase: metal activation, solvent isotope effects, and kinetic mechanism
Biochemistry
37
10478-10487
1998
Haemophilus influenzae, Haemophilus influenzae RD
brenda
Born, T.L.; Blanchard, J.S.
Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
Curr. Opin. Chem. Biol.
3
607-613
1999
Haemophilus influenzae
brenda
Bienvenue, D.L.; Gilner, D.M.; Davis, R.S.; Bennett, B.; Holz, R.C.
Substrate specificity, metal binding properties, and spectroscopic characterization of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae
Biochemistry
42
10756-10763
2003
Haemophilus influenzae
brenda
Davis, R.; Bienvenue, D.; Swierczek, S.I.; Gilner, D.M.; Rajagopal, L.; Bennett, B.; Holz, R.C.
Kinetic and spectroscopic characterization of the E134A- and E134D-altered dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae
J. Biol. Inorg. Chem.
11
206-216
2006
Haemophilus influenzae
brenda
Dea-Ayuela, M.A.; Rama-Iniguez, S.; Bolas-Fernandez, F.
Proteomic analysis of antigens from Leishmania infantum promastigotes
Proteomics
6
4187-4194
2006
Leishmania infantum
brenda
Gillner, D.; Armoush, N.; Holz, R.C.; Becker, D.P.
Inhibitors of bacterial N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) and demonstration of in vitro antimicrobial activity
Bioorg. Med. Chem. Lett.
19
6350-6352
2009
Haemophilus influenzae
brenda
Gillner, D.; Bienvenue, D.; Nocek, B.; Joachimiak, A.; Zachary, V.; Bennett, B.; Holz, R.
The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues
J. Biol. Inorg. Chem.
14
1-10
2009
Haemophilus influenzae
brenda
Nocek, B.P.; Gillner, D.M.; Fan, Y.; Holz, R.C.; Joachimiak, A.
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase
J. Mol. Biol.
397
617-626
2010
Haemophilus influenzae, Haemophilus influenzae (P44514)
brenda
Brunger, A.T.; Das, D.; Deacon, A.M.; Grant, J.; Terwilliger, T.C.; Read, R.J.; Adams, P.D.; Levitt, M.; Schroeder, G.F.
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
Acta Crystallogr. Sect. D
68
391-403
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2014
Haemophilus influenzae
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