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Literature summary for 3.4.16.4 extracted from

  • Dzhekieva, L.; Adediran, S.A.; Herman, R.; Kerff, F.; Duez, C.; Charlier, P.; Sauvage, E.; Pratt, R.F.
    Inhibition of DD-peptidases by a specific trifluoroketone: crystal structure of a complex with the Actinomadura R39 DD-peptidase (2013), Biochemistry, 52, 2128-2138.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
-
Actinomadura sp.

Crystallization (Commentary)

Crystallization (Comment) Organism
in complex with inhibitor (2R)-2-amino-7-oxo-7-[(4,4,4-trifluoro-3-oxobutan-2-yl)amino]heptanoic acid. The inhibitor is covalently bonded to the active serine Ser49, the carbonyl carbon is now tetrahedral, and the ketone oxygen occupies the oxyanion hole, defined by the backbone NH groups of Ser49 and Thr413. The D-methyl group is directed into a hydrophobic pocket comprised residues Gly148, Leu 349 and Met414. Branching from the tetrahedral carbon bonded to Ser49Ogamma, the CF3 group occupies the likely position of a leaving group in the tetrahedral intermediate of a peptidase substrate Actinomadura sp.

Inhibitors

Inhibitors Comment Organism Structure
(2R)-2-amino-7-oxo-7-[(4,4,4-trifluoro-3-oxobutan-2-yl)amino]heptanoic acid i.e. D-alpha-aminopimelyl-(1,1,1-trifluoro-3-amino)butan-2-one Actinomadura sp.

Organism

Organism UniProt Comment Textmining
Actinomadura sp. P39045
-
-

Synonyms

Synonyms Comment Organism
Dac
-
Actinomadura sp.
DD-peptidase
-
Actinomadura sp.

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.00037
-
(2R)-2-amino-7-oxo-7-[(4,4,4-trifluoro-3-oxobutan-2-yl)amino]heptanoic acid pH not specified in the publication, temperature not specified in the publication Actinomadura sp.