8I2E

Crystal structure of Bacillus subtilis LytE in complex with IseA

Summary for 8I2E

• Entry DOI: 10.2210/pdb8i2e/pdb
• Descriptor: Uncharacterized protein YoeB, Probable peptidoglycan endopeptidase LytE (2 entities in total)
• Functional Keywords: dl-endopeptidase, antimicrobial protein-inhibitor complex, antimicrobial protein/inhibitor
• Biological source: Bacillus subtilis subsp. subtilis str. 168; More
• Total number of polymer chains: 4
• Total formula weight: 102057.67

Authors

Tandukar, S.,Kwon, E.,Kim, D.Y. (deposition date: 2023-01-14, release date: 2023-04-05, Last modification date: 2024-11-20)

Primary citation

Tandukar, S.,Kwon, E.,Kim, D.Y.
Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA.
Structure, 31:619-628.e4, 2023

PubMed Abstract: Peptidoglycan, a physical barrier that protects bacteria from the environment, is constantly degraded and resynthesized for remodeling during cell growth and division. Because excessive or insufficient peptidoglycan hydrolysis affects bacterial homeostasis and viability, peptidoglycan degradation must be precisely regulated. In Bacillus subtilis, DL-endopeptidases play an essential role in peptidoglycan remodeling, and their activity is regulated by IseA. Here, we report the crystal structure of peptidoglycan DL-endopeptidase LytE complexed with IseA. In the crystal structure, the inhibitory loop connecting the two lobes of IseA blocks the active site of LytE by mimicking its substrate. Consistently, mutations in the inhibitory loop resulted in the loss of IseA activity. The structure also shows that conformational rearrangements in both LytE and IseA restrict access of the inhibitory loop to the LytE catalytic site. These results reveal an inhibition mechanism of peptidoglycan DL-endopeptidase in which the inhibitory protein mimics the substrate but is not degraded.

PubMed: 36963396
DOI: 10.1016/j.str.2023.02.013

Experimental method

X-RAY DIFFRACTION (3.2 Å)