Information on EC 3.5.1.18 - succinyl-diaminopimelate desuccinylase

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

EC NUMBER
COMMENTARY
3.5.1.18
-
RECOMMENDED NAME
GeneOntology No.
succinyl-diaminopimelate desuccinylase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
N-succinyl-LL-2,6-diaminoheptanedioate + H2O = succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
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
-, P44514
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hydrolysis of peptide bond
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Lysine biosynthesis
-
lysine biosynthesis I
-
Metabolic pathways
-
Microbial metabolism in diverse environments
-
SYSTEMATIC NAME
IUBMB Comments
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Cgl1109
Corynebacterium glutamicum 534
Q59284
-
-
dapE-encoded N-succinyl-LL-diaminopimelic acid desuccinylase
-
-
N-succinyl-L,L-diaminopimelic acid desuccinylase
-
-
N-succinyl-L,L-diaminopimelic acid desuccinylase
P44514
-
N-succinyl-L,L-diaminopimelic acid desuccinylase
-
-
N-succinyl-L-alpha,epsilon-diaminopimelic acid deacylase
-
-
-
-
SDAP
-
-
-
-
sDap desuccinylase
-
-
-
-
succinyl-diaminopimelate desuccinylase
Q59284
-
succinyl-diaminopimelate desuccinylase
Corynebacterium glutamicum 534
Q59284
-
-
succinyl-diaminopimelate desuccinylase
-
-
succinyldiaminopimelate desuccinylase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9024-94-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
No.48292
-
-
Manually annotated by BRENDA team
Bacillus cereus No.48292
No.48292
-
-
Manually annotated by BRENDA team
Corynebacterium diphtheriae P.W.8
P.W.8
-
-
Manually annotated by BRENDA team
Corynebacterium glutamicum 534
-
Q59284
UniProt
Manually annotated by BRENDA team
M-26-26; wild type ATCC 9637
-
-
Manually annotated by BRENDA team
Escherichia coli M-26-26
M-26-26
-
-
Manually annotated by BRENDA team
Haemophilus influenzae RD
RD
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
DapE is involved in the meso-diaminopimelate (mDAP)/lysine biosynthetic pathway
metabolism
-, P44514
DapE is involved in the meso-diaminopimelate, mDAP/lysine biosynthetic pathway
physiological function
-
DapE is a critical bacterial enzyme for the construction of the bacterial cell wall.
physiological function
-, P44514
DapE is essential for cell growth and proliferation
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
P44514
-
-
-
?
N-succinyl-DL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
Haemophilus influenzae, Haemophilus influenzae RD
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-, Q59284
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
i.e. N-succinyl-L,L-diaminopimelic acid
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
Escherichia coli M-26-26
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
Corynebacterium glutamicum 534
Q59284
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
Haemophilus influenzae RD
-
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
Bacillus cereus No.48292, Corynebacterium diphtheriae P.W.8
-
-
-
-
?
N-succinyl-LL-2,6-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-diaminopimelate + H2O
?
show the reaction diagram
-
-
-
-
?
N-succinyl-LL-diaminopimelic acid + H2O
?
show the reaction diagram
-
-
-
-
?
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
?
show the reaction diagram
-
high stereospecificity
-
?
additional information
?
-
-
kinetic mechanism
-
-
-
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
-
-
-
additional information
?
-
Haemophilus influenzae RD
-
kinetic mechanism
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
-
-
-
?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
P44514
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-, Q59284
-
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
-
i.e. N-succinyl-L,L-diaminopimelic acid
-
-
?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
show the reaction diagram
Corynebacterium glutamicum 534
Q59284
-
-
-
?
additional information
?
-
-
kinetic mechanism
-
-
-
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
-
-
-
additional information
?
-
Haemophilus influenzae RD
-
kinetic mechanism
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Al3+
-
required
Cd2+
-
65% of activity with Zn2+
Co2+
-
required and most active as a cofactor
Co2+
-
125% of activity with Zn2+
Co2+
-
can substitute for Zn2+
Fe3+
-
required
Mg2+
-
required
Mn2+
-
required
Mn2+
-
20% of activity with Zn2+
Ni2+
-
required
sulfate
-, P44514
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+
-
required
Zn2+
-
required
Zn2+
-
100% of activity
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+
-, P44514
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+
-
the enzyme possesses a catalytic domain with a di-zinc active site
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(2-carboxyethyl)-phosphonic acid
-
slight inhibition
2-thiopheneboronic acid
-
noncompetitive
-
3-mercaptobenzoic acid
-
-
-
aceto-hydroxamic acid
-
slight inhibition
D,L-diaminopimelic acid
-
competitive
D-captopril
-
-
-
D-penicillamine
-
competitive
delta-mercaptobutyric acid
-
-
-
enalapril
-
maleate salt, slight inhibition
L,L-diaminopimelic acid
-
competitive
L-captopril
-
-
-
L-captopril
-
low-micromolar inhibitor, DapE is not the main target of L-captopril inhibition
-
N-(benzyloxycarbonyl)hydroxylamine
-
slight inhibition
-
N-phenyl-thiourea
-
slight inhibition
Phenylboronic acid
-
competitive
L-Penicillamine
-
-
additional information
-
no or poor inhibition by butylboronic acid, 4-carboxyphenylboronic acid, and 3-carboxyphenylboronic acid
-
additional information
-, P44514
design of structure-based, catalytic inhibitors, overview
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.26
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, ZnCo-loaded enzyme
0.73
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, Zn-loaded enzyme; pH 7.5, 30C, ZnZn-loaded enzyme
0.74
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, CoZn-loaded enzyme
0.99
-
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30C, CoCo-loaded enzyme; pH 7.5, 30C, Co-loaded enzyme
730
-
N-succinyl LL-diaminopimelic acid
-, P44514
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+
1.3
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
37C, pH 8.1
1.3
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Zn2+
1.5
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
37C, pH 8.1, in the presence of Co2+
1.6
-
N-succinyl-LL-2,6-diaminoheptanedioate
-
in the presence of Co2+
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, 30C, wild-type enzyme
-
1.4
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, 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
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
140
-
N-succinyl LL-diaminopimelic acid
-, P44514
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
1.5
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, mutant H67A
-
140
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, 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
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.1
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, mutant H67A
0
204
-
N-succinyl-LL-2,6-diaminopimelic acid
-
pH 7.5, 30C, wild-type enzyme
0
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
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
-
0.0018
-
L-captopril
-
pH not specified in the publication, temperature not specified in the publication
-
0.0018
-
L-captopril
-
pH and 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
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.62
-
(2-carboxyethyl)-phosphonic acid
-
pH not specified in the publication, temperature not specified in the publication
0.092
-
2-thiopheneboronic acid
-
pH not specified in the publication, temperature not specified in the publication
-
0.034
-
3-mercaptobenzoic acid
-
pH not specified in the publication, temperature not specified in the publication
-
1
-
aceto-hydroxamic acid
-
above, pH not specified in the publication, temperature not specified in the publication
0.042
-
D-captopril
-
pH not specified in the publication, temperature not specified in the publication
-
0.05
-
D-penicillamine
-
pH not specified in the publication, temperature not specified in the publication
0.043
-
delta-mercaptobutyric acid
-
pH not specified in the publication, temperature not specified in the publication
-
1
-
enalapril
-
above, pH not specified in the publication, temperature not specified in the publication
0.0033
-
L-captopril
-
pH not specified in the publication, temperature not specified in the publication
-
0.0033
-
L-captopril
-
pH and temperature not specified in the publication
-
0.0137
-
L-Penicillamine
-
pH not specified in the publication, temperature not specified in the publication
1
-
N-(benzyloxycarbonyl)hydroxylamine
-
above, pH not specified in the publication, temperature not specified in the publication
-
0.01
-
N-phenyl-thiourea
-
above, pH not specified in the publication, temperature not specified in the publication
0.107
-
Phenylboronic acid
-
pH not specified in the publication, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.17
-
-
mutant enzyme E134D at pH 7.5
180
-
-
wild type enzyme at pH 7.5
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
9
-
pH 6: 60%, pH 9: 65% of maximal activity
6
9
-
activity below pH 6.0 was not observed
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
assay at
PDB
SCOP
CATH
ORGANISM
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)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
41500
-
-
SDS-PAGE
83000
-
-, P44514
about
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-, P44514
2 * 41500, SDS-PAGE
homodimer
-
2 * 41600, estimated from amino acid sequence; 2 * 42000, SD-PAGE
monomer
-
1 * 41350, electrospray mass spectroscopy
monomer
Haemophilus influenzae RD
-
1 * 41350, electrospray mass spectroscopy
-
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
-, P44514
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
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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 20C
-, Q59284
ultrapure recombinant DapE with one and two zinc ions bound in the active site, respectively, at 16C, 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
-, P44514
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
9
-
activity below pH 6.0 was not observed
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
fast-flow Q-sepharose anionexchange column chromatography
-
recombinant wild-type enzyme and mutants from Escherichia coli BL21
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli
-
expression in Escherichia coli
-
gene dapE, expression of wild-type enzyme and mutants in Escherichia coli BL21, subcloning in Escherichia coli JM109
-
expressed in Escherichia coli XL1-Blue cells and in Salmonella enterica strain TN5911
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
E134A
-
Glu134 replaced by alanine
E134D
-
Glu134 replaced by aspartate
H349A
-
site-directed mutagenesis, inactive mutant
H67A
-
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+
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
drug development
-, P44514
development of antimicrobial agents that target DapE
drug development
-
protein may be potential target for developing a vaccine against Leishmania infantum