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.

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

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	a

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