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Information on EC 3.5.1.18 - succinyl-diaminopimelate desuccinylase
for references in articles please use BRENDA:EC3.5.1.18
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EC Tree 3 Hydrolases
3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
3.5.1 In linear amides
3.5.1.18 succinyl-diaminopimelate desuccinylase
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
- 3.5.1.18
- haemophilus
- l-captopril
- peptidoglycan
-
meso-diaminopimelic
- acetylornithine
-
metallohydrolase
- drug development
- medicine
Reaction Schemes
showSynonyms
n-succinyl-l,l-diaminopimelic acid desuccinylase, succinyl-diaminopimelate desuccinylase, hidape, succinyldiaminopimelate desuccinylase, cgl1109, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Cgl1109
DapE
HiDapE
N-succinyl-L,L-diaminopimelic acid desuccinylase
N-succinyl-L-alpha,epsilon-diaminopimelic acid deacylase
-
-
-
-
Rv1202
SDAP
-
-
-
-
sDap desuccinylase
-
-
-
-
succinyl-diaminopimelate desuccinylase
succinyldiaminopimelate desuccinylase
-
-
-
-
N-succinyl-L,L-diaminopimelic acid 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 SOURCE
PATHWAYS
BRENDA
MetaCyc
L-lysine biosynthesis I
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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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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
?
-
Substrates: high stereospecificity
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?
N-succinyl-LL-2,6-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-diaminopimelic acid + H2O
?
-
Substrates: -
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?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-DL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-DL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: a combination of different computational methods, such as protein-ligand docking, MD simulations, free-energy analysis with the MM-PBSA method, and hybrid QM/MM calculations, to provide a detailed account of the substrate binding and catalytic reaction in three important mutants of DapE and compared them to the action of the wt-DapE
Products: -
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N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: a combination of different computational methods, such as protein-ligand docking, MD simulations, free-energy analysis with the MM-PBSA method, and hybrid QM/MM calculations, to provide a detailed account of the substrate binding and catalytic reaction in three important mutants of DapE and compared them to the action of the wt-DapE
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: i.e. N-succinyl-L,L-diaminopimelic acid
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
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?
additional information
?
-
-
Substrates: acetylornithine deacetylase, succinyldiaminopimelate desuccinylase and carboxypeptidase G2 are evolutionarily related
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?
additional information
?
-
-
Substrates: kinetic mechanism
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?
additional information
?
-
-
Substrates: structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
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?
additional information
?
-
-
Substrates: kinetic mechanism
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?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
Products: -
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?
N-succinyl LL-diaminopimelic acid + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: -
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
-
Substrates: i.e. N-succinyl-L,L-diaminopimelic acid
Products: -
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?
N-succinyl-LL-2,6-diaminoheptanedioate + H2O
succinate + LL-2,6-diaminoheptanedioate
Substrates: -
Products: -
Products: -
?
additional information
?
-
-
Substrates: acetylornithine deacetylase, succinyldiaminopimelate desuccinylase and carboxypeptidase G2 are evolutionarily related
Products: -
Products: -
?
additional information
?
-
-
Substrates: kinetic mechanism
Products: -
Products: -
?
additional information
?
-
-
Substrates: structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis
Products: -
Products: -
?
additional information
?
-
-
Substrates: kinetic mechanism
Products: -
Products: -
?
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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+
Co2+
-
metal-dependent enzyme (Zn2+ or Co2+). Determination of metal stoichiometry by ICP-AES indicates one tightly bound metal ion, while sequence homologies suggest the presence of two metal binding sites
Co2+
EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled
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+
-
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+
-
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+
-
metal-dependent enzyme (Zn2+ or Co2+). Determination of metal stoichiometry by ICP-AES indicates one tightly bound metal ion, while sequence homologies suggest the presence of two metal binding sites
Zn2+
two Zn metal centers are essential to the catalytic action of the DapE enzyme. His67, His349, and Glu134 residues in the active site
Zn2+
untreated enzyme contains 0.8 Zn2+ per monomer and was enzymatically active
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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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-amino-6-[(2-methylpropanoyl)amino]heptanedioic acid
-
slight inhibition
2-thiopheneboronic acid
22.3% inhibition at 10 mM, non-competitive inhibitor
L-captopril
99.96%, 26.67% and 23.34% inhibition at 10 mM, 3 mM, and 1 mM
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
-
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
-
additional information
Tanimoto-based similarity searching in the PubChem Database with DapE substrate N-succinyl-LL-2,6-diaminoheptanedioate as a query molecule, followed by fragment-based docking approach using GLIDE XP identifies two potential substrate-competitive small molecule inhibitors of DapE. These new molecules may provide a starting point to search for novel therapeutics
-
additional information
-
Tanimoto-based similarity searching in the PubChem Database with DapE substrate N-succinyl-LL-2,6-diaminoheptanedioate as a query molecule, followed by fragment-based docking approach using GLIDE XP identifies two potential substrate-competitive small molecule inhibitors of DapE. These new molecules may provide a starting point to search for novel therapeutics
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Bacterial Infections
Loss of Catalytic Activity in the E134D, H67A, and H349A Mutants of DapE: Mechanistic Analysis with QM/MM Investigation.
Tuberculosis
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis.
Tuberculosis
Reconstruction of diaminopimelic acid biosynthesis allows characterisation of Mycobacterium tuberculosis N-succinyl-L,L-diaminopimelic acid desuccinylase.
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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
0.73
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
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, Co-loaded enzyme
0.99
(2S,6S)-2-amino-6-[(3-carboxypropanoyl)amino]heptane-dioic acid
-
pH 7.5, 30°C, CoCo-loaded enzyme
0.03109
N-succinyl-LL-2,6-diaminoheptanedioate
pH 8.0, 37°C
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
-
25°C, pH 7.6, 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
-
25°C, pH 7.6, 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
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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
200
N-succinyl-LL-2,6-diaminoheptanedioate
-
25°C, pH 7.6, in the presence of Zn2+
370
N-succinyl-LL-2,6-diaminoheptanedioate
-
25°C, pH 7.6, in the presence of Co2+
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
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 - 8.9
-
the maximal velocity is independent of pH above pH 7 when Zn2+ is used to activate the enzyme
7.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 8.9
-
the maximal velocity is independent of pH above pH 7 when Zn2+ is used to activate the enzyme. Below pH 7, the maximum velocity decreases with an apparent slope of 1, indicating that protonation of a single ionizable group, exhibiting a pK value of 6.6
6 - 9
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
