Document Type
Article
Publication Date
3-16-2021
Publication Title
Biochemistry
Volume
60
Issue
12
Pages
908–917
Publisher Name
ACS Publications
Abstract
We report the atomic-resolution (1.3 Å) 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.
Recommended Citation
Kochert, Matthew; Nocek, Boguslaw P.; Habeeb Mohammad, Thahani S.; Gild, Elliot; Lovato, Kaitlyn; Heath, Tahirah K.; Holz, Richard C.; Olsen, Kenneth W.; and Becker, Daniel P. Ph.D.. Atomic-Resolution 1.3 Å Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE. Biochemistry, 60, 12: 908–917, 2021. Retrieved from Loyola eCommons, Chemistry: Faculty Publications and Other Works, http://dx.doi.org/10.1021/acs.biochem.0c00926
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This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.
Copyright Statement
© American Chemical Society, 2021.
Comments
Author Posting © American Chemical Society, 2021. This is the author's version of the work. This article is posted here by permission of American Chemical Society for personal use, not for redistribution. The article was published in Biochemistry, Volume 60, Issue 12, March 2021, https://doi.org/10.1021/acs.biochem.0c00926