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Literature summary extracted from

  • 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 (2010), J. Mol. Biol., 397, 617-626.
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
3.5.1.18 drug development development of antimicrobial agents that target DapE Haemophilus influenzae

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.18 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 Haemophilus influenzae

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.18 additional information design of structure-based, catalytic inhibitors, overview Haemophilus influenzae

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.18 730
-
 N-succinyl LL-diaminopimelic acid pH not specified in the publication, temperature not specified in the publication Haemophilus influenzae

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.18 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 Haemophilus influenzae
3.5.1.18 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 Haemophilus influenzae

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.5.1.18 41500
-
 2 * 41500, SDS-PAGE Haemophilus influenzae
3.5.1.18 83000
-
 about Haemophilus influenzae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.18 N-succinyl LL-diaminopimelic acid + H2O Haemophilus influenzae
-
 succinate + LL-2,6-diaminoheptanedioate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.18 Haemophilus influenzae P44514 gene dapE
-

Reaction

EC Number Reaction Comment Organism Reaction ID
3.5.1.18 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 Haemophilus influenzae
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.18 N-succinyl LL-diaminopimelic acid + H2O
-
 Haemophilus influenzae succinate + LL-2,6-diaminoheptanedioate
-
 ?

Subunits

EC Number Subunits Comment Organism
3.5.1.18 dimer 2 * 41500, SDS-PAGE Haemophilus influenzae
3.5.1.18 More 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 Haemophilus influenzae

Synonyms

EC Number Synonyms Comment Organism
3.5.1.18 DapE
-
 Haemophilus influenzae
3.5.1.18 N-succinyl-L,L-diaminopimelic acid desuccinylase
-
 Haemophilus influenzae

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.18 140
-
 N-succinyl LL-diaminopimelic acid pH not specified in the publication, temperature not specified in the publication Haemophilus influenzae

General Information

EC Number General Information Comment Organism
3.5.1.18 metabolism DapE is involved in the meso-diaminopimelate, mDAP/lysine biosynthetic pathway Haemophilus influenzae
3.5.1.18 physiological function DapE is essential for cell growth and proliferation Haemophilus influenzae