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Enzyme Nomenclature
Information on EC 3.5.1.18 - succinyl-diaminopimelate desuccinylase
for references in articles please use BRENDA:EC3.5.1.18
Word Map on EC 3.5.1.18
- 3.5.1.18
- influenzae
-
haemophilus
- peptidoglycan
- l-captopril
-
deacetylase
-
carboxypeptidase
-
meso-diaminopimelic
- glutamicum
- acetylornithine
-
metallohydrolase
- drug development
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
3.5.1.18
-
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RECOMMENDED NAME
GeneOntology No.
succinyl-diaminopimelate desuccinylase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate
structure-activity relationship and catalytic mechanism of peptide bond cleavage by DapE enzymes, overview. The catalytic domain is composed of residues 1-179 and 293-376
N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate
the catalytic reaction progresses via a general acid-base hydrolysis mechanism where Glu134 first acts as a Lewis base by activating the catalytic water molecule in the active site, followed by guiding the resulting hydroxyl ion for a nucleophilic attack on the substrate, and finally acts as a Lewis acid by donating a proton to the substrate. Catalytic mechanism and intermediates and transition states, hybrid QM/MM computational method analysis, overview. A conformational change in the side chain of Asp100, which bridges the two Zn centers of the enzyme, is observed which facilitates the enzymatic action by lowering the activation energy and leads to the formation of a different intermediate during the catalytic reaction. The nucleophilic attack is the rate determining step
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of peptide bond
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
-
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CAS REGISTRY NUMBER
COMMENTARY
9024-94-6
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
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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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-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
?
-
high stereospecificity
-
?
N-succinyl-LL-2,6-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
-
-
-
-
?
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
?
-
-
structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
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
?
-
-
structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
-
-
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Mn2+
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
Zn2+
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+
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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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-amino-6-[(2-methylpropanoyl)amino]heptanedioic acid
-
slight inhibition
L-captopril
-
low-micromolar inhibitor, DapE is not the main target of L-captopril inhibition
additional information
-
no or poor inhibition by butylboronic acid, 4-carboxyphenylboronic acid, and 3-carboxyphenylboronic acid
-
additional information
design of structure-based, catalytic inhibitors, overview
-
additional information
-
mono-N-acyl derivatives of 2,6-diaminopimelic acid are no effective N-succinyl-L,L-diaminopimelic acid desuccinylase inhibitors, overview. No inhibition by 2-amino-6-(butanoylamino)heptanedioic acid, 2-amino-6-[(2,2-dimethylpropanoyl)amino]heptanedioic acid, 2-amino-6-(pentanoylamino)heptanedioic acid, 2-amino-6-(benzoylamino)heptanedioic acid, 2-amino-6-[(4-carboxybutanoyl)amino]heptanedioic acid, 2-amino-6-[(4-carboxy-3-methylbutanoyl)amino]heptanedioic acid, 2-amino-6-[(4-carboxy-3,3-dimethylbutanoyl)amino]heptanedioic acid, 2-amino-6-[(4-carboxy-2,2,3,3-tetrafluorobutanoyl)amino]heptanedioic acid, 2-amino-6-[[(2E)-4-methoxy-4-oxobut-2-enoyl]amino]heptanedioic acid, 2-amino-6-[(3-ethoxy-3-oxopropanoyl)amino]heptanedioic acid, and 2-amino-6-[[(2R)-4-methoxy-2-methylpent-4-enoyl]amino]heptanedioic acid
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
730
N-succinyl LL-diaminopimelic acid
pH not specified in the publication, temperature not specified in the publication
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
1.5
N-succinyl-LL-2,6-diaminoheptanedioate
-
37°C, pH 8.1, 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
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
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
140
N-succinyl LL-diaminopimelic acid
pH not specified in the publication, temperature not specified in the publication
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
-
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.1
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30°C, mutant H67A
-
204
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30°C, wild-type enzyme
-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.8
(2-carboxyethyl)-phosphonic acid
-
pH not specified in the publication, temperature not specified in the publication
0.067
2-thiopheneboronic acid
-
pH not specified in the publication, temperature not specified in the publication
0.0046
L-Penicillamine
-
pH not specified in the publication, temperature not specified in the publication
0.0569
phenylboronic acid
-
pH not specified in the publication, temperature not specified in the publication
0.0018
L-captopril
-
pH not specified in the publication, temperature not specified in the publication
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 9
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
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)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
28700
41500
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
-
2 * 41600, estimated from amino acid sequence; 2 * 42000, SD-PAGE
monomer
additional information
dimer
-
the DapE enzyme exists in a dimeric form with each monomer consisting of a catalytic and dimerization domain
dimer
-
the enzyme is composed of catalytic and dimerization domains, the dimerization domain in DapE enzymes is required for catalysis
dimer
the enzyme is composed of catalytic and dimerization domains, the dimerization domain in DapE enzymes is required for catalysis
additional information
-
three-dimensional homology structure of the DapE, based on the crystal structure of the DapE from Neisseria meningitidis as template and and superimposed on the structure of the aminopeptidase from Aeromonas proteolytica, overview
additional information
the core of the catalytic domain consists of an eight-stranded twisted beta-sheet that is sandwiched between seven alpha-helices, active site structure and structure-activity relationship, overview
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
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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
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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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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3)/pMAGIC by nickel affinity chromatography and gel filtration
recombinant N-terminally His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)/pMAGIC by nickel affinity chromatography and gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli XL1-Blue cells and in Salmonella enterica strain TN5911
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gene dapE, expression of wild-type enzyme and mutants in Escherichia coli BL21, subcloning in Escherichia coli JM109
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gene dape, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) chaperone combination 3 (cc3) cells, which co-express the chaperones GroEL and GroES in order to increase the yield of soluble protein expression
gene dapE, recombinant expression of N-terminally His6-tagged enzyme, containing a TEV protease recognition site followed by the DapE catalytic domain, in an Escherichia coli strain BL21(DE3) derivative that harbors the pMAGIC plasmid encoding one rare Escherichia coli Arg tRNA (covering codons AGG/AGA)
gene dapE, recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes, containing a TEV protease recognition site followed by the DapE catalytic domain, in an Escherichia coli strain BL21(DE3) derivative that harbors the pMAGIC plasmid encoding one rare Escherichia coli Arg tRNA (covering codons AGG/AGA)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H67A
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site-directed mutagenesis, the mutant shows 180fold decreased activity compred to the wild-type enzyme. Approximately 70% of the maximal catalytic activity is recovered after the addition of 1 equiv of Zn2+
T325A
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site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
T325S
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site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
additional information
additional information
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construction of dimerization domain deletion mutants, that all show no activity
additional information
construction of dimerization domain deletion mutants, that all show no activity
additional information
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construction of dimerization domain deletion mutants, that all show no activity
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
drug development
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protein may be potential target for developing a vaccine against Leishmania infantum
drug development
development of antimicrobial agents that target DapE
Show AA Sequence (10331 entries)
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LINKS TO OTHER DATABASES (specific for EC-Number 3.5.1.18)
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