14289-34-0Relevant articles and documents
Atomic-Resolution 1.3 ? Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE
Kochert, Matthew,Nocek, Boguslaw P.,Habeeb Mohammad, Thahani S.,Gild, Elliot,Lovato, Kaitlyn,Heath, Tahirah K.,Holz, Richard C.,Olsen, Kenneth W.,Becker, Daniel P.
, p. 908 - 917 (2021/04/07)
We report the atomic-resolution (1.3 ?) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the starting point for targeted molecular dynamics experiments revealing the conformational change from the open form to the closed form that occurs when DapE binds l,l-SDAP and cleaves the amide bond. These simulations demonstrated closure from the open to the closed conformation, the change in RMS throughout the closure, and the independence in the movement of the two DapE subunits. This conformational change occurred in two phases with the catalytic domains moving toward the dimerization domains first, followed by a rotation of catalytic domains relative to the dimerization domains. Although there were no targeting forces, the substrate moved closer to the active site and bound more tightly during the closure event.
Synthesis of bis-α,α′-amino acids through diastereoselective bis-alkylations of chiral Ni(ii)-complexes of glycine
Wang, Jiang,Liu, Hong,Ace?a, José Luis,Houck, Daniel,Takeda, Ryosuke,Moriwaki, Hiroki,Sato, Tatsunori,Soloshonok, Vadim A.
, p. 4508 - 4515 (2013/08/23)
The Ni(ii) complex derived from glycine Schiff base with (S)-N-(benzylprolyl)-2-aminobenzophenone can be effectively alkylated with α,ω-dibromide reagents to furnish the corresponding bis-alkylated products. This method presents a direct approach for the preparation of the corresponding bis-α,α′-amino acids with high biological importance. Heterogeneous (phase-transfer) as well as homogeneous conditions for the alkylation reactions have been investigated and the latter proved to be more efficient in terms of stereochemical outcome. In particular, alkylation of the glycine Schiff base Ni(ii) complex with 1,3-dibromopropane followed by acid-catalysed hydrolysis of the resulting bis-alkylation product, allowed for the preparation of naturally occurring (2S,6S)-diaminopimelic acid in high overall yield. The Royal Society of Chemistry 2013.
Structural Basis for Catalysis by the Mono- and Dimetalated Forms of the dapE-Encoded N-succinyl-l,l-Diaminopimelic Acid Desuccinylase
Nocek, Boguslaw P.,Gillner, Danuta M.,Fan, Yao,Holz, Richard C.,Joachimiak, Andrzej
experimental part, p. 617 - 626 (2011/04/26)
Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-l,l-diaminopimelic acid to l,l-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors.
