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 a 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 (L,L-SDAP) 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.The meso-diaminopimelate (mDAP)/lysine biosynthetic pathway offers several potential antibacterial enzyme targets that have yet to be explored. 1, 2 , 3 One of the products of this pathway, lysine, is required in protein synthesis and is also used in the peptidoglycan layer of Gram-positive bacterial cell walls. A second product of this pathway, mDAP is an essential component of the peptidoglycan cell wall for Gram-negative bacteria, providing a link between polysaccharide strands. It has been shown that deletion of the gene encoding one of the enzymes © 2010 Elsevier Ltd. All rights reserved. * Address correspondence to: Department of Chemistry, Loyola University-Chicago, 1068 W. Sheridan Rd., Chicago, IL 60626, Phone (773) Fax: (773) Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. DapE.6 ,11 ,12 ,16 ,17 Interestingly, it has been reported that the "as purified" DapE enzyme contains only one tightly bound Zn(II) ion and exhibits ~60% of its total activity, similar to AAP. 6, 12 Thus, both metal ions seem to be required for full enzymatic activity, but their individual catalytic roles appear to differ markedly. NIH Public AccessA major lim...

No abstract

In this review, we summarize the recent literature on dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) enzymes, with an emphasis on structure–function studies that provide insight into the catalytic mechanism. Crystallographic data have also provided insight into residues that might be involved in substrate and hence inhibitor recognition and binding. These data have led to the design and synthesis of several new DapE inhibitors, which are described along with what is known about how inhibitors interact with the active site of DapE enzymes, including the efficacy of a moderately strong DapE inhibitor.