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Structural basis for the hydrolytic activity of the transpeptidase-like protein DpaA to detach Braun’s lipoprotein from peptidoglycan

Lookup NU author(s): Dr Victor Hernandez-RocamoraORCiD, Professor Waldemar Vollmer

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2023 Wang et al.The peptidoglycan layer is a defining characteristic of bacterial cells, providing them with structural support and osmotic protection. In Escherichia coli, this layer is linked to the outer membrane via the abundant membrane-anchored protein Lpp, known as Braun’s lipoprotein, with LD-transpeptidases LdtA, LdtB, and LdtC catalyzing the attachment. However, one distinctive member of the YkuD-type transpeptidase family, LdtF (recently renamed DpaA), carries out the opposite reaction of detaching Lpp from the peptidoglycan layer. In this study, we report the crystal structure of DpaA, which reveals the enzyme’s ability to cleave, rather than form, the Lpp-peptidoglycan linkage. Assays with purified peptidoglycan-Lpp as the substrate and chemically synthesized compounds suggest that DpaA’s shallow L-shaped active site can only accommodate and cleave the peptidoglycan-Lpp cross-link with a constrained conformation. This study provides insights into how homologous Ldt enzymes can perform opposing chemical reactions.

Publication metadata

Author(s): Wang H-J, Hernandez-Rocamora VM, Kuo C-I, Hsieh K-Y, Lee S-H, Ho M-R, Tu Z, Vollmer W, Chang C-I

Publication type: Article

Publication status: Published

Journal: mBio

Year: 2023

Volume: 14

Issue: 5

Print publication date: 31/10/2023

Online publication date: 13/10/2023

Acceptance date: 21/08/2023

Date deposited: 28/11/2023

ISSN (print): 2161-2129

ISSN (electronic): 2150-7511

Publisher: American Society for Microbiology

URL: https://doi.org/10.1128/mbio.01379-23

DOI: 10.1128/mbio.01379-23

Data Access Statement: The structural factors and coordinates have been deposited in the Protein Data Bank under the accession code 8IKR. The docking model has been deposited in ModelArchive and is available at https://modelarchive.org/doi/10.5452/ma-y2f7x.

PubMed id: 37830798

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