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Literature summary for 3.5.1.18 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

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

Crystallization (Commentary)

Crystallization (Comment) Organism
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

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

KM Value [mM]

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

Metals/Ions

Metals/Ions Comment Organism Structure
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
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]

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

Natural Substrates/ Products (Substrates)

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

Organism

Organism UniProt Comment Textmining
Haemophilus influenzae P44514 gene dapE
-

Reaction

Reaction Comment Organism Reaction ID
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

Substrates and Products (Substrate)

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

Subunits

Subunits Comment Organism
dimer 2 * 41500, SDS-PAGE Haemophilus influenzae
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

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

Turnover Number [1/s]

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

General Information

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