7KGM

C. rodentium YcbB - ertapenem complex

Summary for 7KGM

• Entry DOI: 10.2210/pdb7kgm/pdb
• Descriptor: Putative exported protein, (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid (3 entities in total)
• Functional Keywords: l, d-transpeptidase, antibiotic, transferase
• Biological source: Citrobacter rodentium (strain ICC168)
• Total number of polymer chains: 1
• Total formula weight: 63809.37

Authors

Caveney, N.A.,Strynadka, N.C.J. (deposition date: 2020-10-17, release date: 2020-11-25, Last modification date: 2023-10-18)

Primary citation

Caveney, N.A.,Serapio-Palacios, A.,Woodward, S.E.,Bozorgmehr, T.,Caballero, G.,Vuckovic, M.,Deng, W.,Finlay, B.B.,Strynadka, N.C.J.
Structural and Cellular Insights into the l,d-Transpeptidase YcbB as a Therapeutic Target in Citrobacter rodentium, Salmonella Typhimurium, and Salmonella Typhi Infections.
Antimicrob.Agents Chemother., 65:-, 2021

PubMed Abstract: The bacterial cell wall plays a key role in viability and is an important drug target. The cell wall is made of elongated polymers that are cross-linked to one another to form a load-bearing mesh. An alternative cell wall cross-linking mechanism used by the l,d-transpeptidase YcbB has been implicated in the stress-regulated roles of β-lactam resistance, outer membrane defect rescue, and typhoid toxin release. The role for this stress-linked cross-linking in the context of a host infection was unclear. Here, we resolve the crystallographic structures of both Typhi YcbB and YcbB acylated with ertapenem that delineate the conserved structural characteristics of YcbB. In parallel, we show that the general involvement of YcbB in peptidoglycan reinforcement under conditions of bacterial outer envelope stress does not play a significant role in acute infections of mice by and Typhimurium. Cumulatively, in this work we provide a foundation for the development of novel YcbB-specific antibacterial therapeutics to assist in treatment of increasingly drug-resistant Typhi infections.

PubMed: 33139287
DOI: 10.1128/AAC.01592-20

Experimental method

X-RAY DIFFRACTION (2.6 Å)