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Literature summary extracted from

  • Dutta, D.; Mishra, S.
    The structural and energetic aspects of substrate binding and the mechanism of action of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) investigated using a hybrid QM/MM method (2014), Phys. Chem. Chem. Phys., 16, 26348-26358.
    View publication on PubMed

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.18 Zn2+ di-nuclear Zn2+ enzyme, the side chain of Asp100 bridges the two Zn centers of the enzyme 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-2,6-diaminoheptanedioate + H2O Haemophilus influenzae
-
 succinate + LL-2,6-diaminoheptanedioate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.18 Haemophilus influenzae
-
 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 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 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-2,6-diaminoheptanedioate + H2O
-
 Haemophilus influenzae succinate + LL-2,6-diaminoheptanedioate
-
 ?

Subunits

EC Number Subunits Comment Organism
3.5.1.18 dimer the DapE enzyme exists in a dimeric form with each monomer consisting of a catalytic and dimerization domain 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

General Information

EC Number General Information Comment Organism
3.5.1.18 metabolism the enzyme is part of the lysine biosynthetic pathway which is indispensable for bacterial survival Haemophilus influenzae
3.5.1.18 additional information residues Arg178, Thr325, and Asn345 play a role in substrate identification and stabilization of the enzyme active site. The glycine rich loop, Gly322-Ser326, facilitates tight binding of the substrate in the enzyme active site. Computational structure modeling by quantum mechanics/molecular mechanics calculations using the enzyme crystal structure PDB ID 3IC1 Haemophilus influenzae