Structural Basis for Catalysis by the Mono- and Dimetalated Forms of the dapE-Encoded N-succinyl-L,L-Diaminopimelic Acid Desuccinylase

Authors

Boguslaw P. Nocek, Argonne National LaboratoryFollow
Danuta Gillner, Loyola University Chicago
Yao Fan, Argonne National Laboratory
Richard C. Holz, Marquette UniversityFollow
Andzrej Joachimiak, Argonne National Laboratory

Document Type

Article

Publication Date

4-2-2010

Source Publication

Journal of Molecular Biology

Source ISSN

0022-2836

Abstract

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.

Comments

Accepted version. Journal of Molecular Biology. Vol. 397, No. 3 (April 2, 2010): 617-626. DOI. © 2010 Elsevier Ltd. Used with permission.

Richard C. Holz was affiliated with Loyola University-Chicago at the time of publication.

Recommended Citation

Nocek, Boguslaw P.; Gillner, Danuta; Fan, Yao; Holz, Richard C.; and Joachimiak, Andzrej, "Structural Basis for Catalysis by the Mono- and Dimetalated Forms of the dapE-Encoded N-succinyl-L,L-Diaminopimelic Acid Desuccinylase" (2010). Chemistry Faculty Research and Publications. 286.
https://epublications.marquette.edu/chem_fac/286