Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI

Shen Wang, Chun-Hsiang Huang, Te-Sheng Lin, Yi-Qi Yeh, Yun-Sheng Fan, Si-Wei Wang, Hsi-Ching Tseng, Shing-Jong Huang, Yu-Yang Chang, U-Ser Jeng, Chung-I Chang and Shiou-Ru Tzeng ()
Additional contact information
Shen Wang: National Taiwan University
Chun-Hsiang Huang: National Synchrotron Radiation Research Center
Te-Sheng Lin: National Taiwan University
Yi-Qi Yeh: National Synchrotron Radiation Research Center
Yun-Sheng Fan: National Taiwan University
Si-Wei Wang: National Taiwan University
Hsi-Ching Tseng: National Taiwan University
Shing-Jong Huang: National Taiwan University
Yu-Yang Chang: National Taiwan University
U-Ser Jeng: National Synchrotron Radiation Research Center
Chung-I Chang: Academia Sinica
Shiou-Ru Tzeng: National Taiwan University

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Peptidoglycan (PG) sacculi surround the cytoplasmic membrane, maintaining cell integrity by withstanding internal turgor pressure. During cell growth, PG endopeptidases cleave the crosslinks of the fully closed sacculi, allowing for the incorporation of new glycan strands and expansion of the peptidoglycan mesh. Outer-membrane-anchored NlpI associates with hydrolases and synthases near PG synthesis complexes, facilitating spatially close PG hydrolysis. Here, we present the structure of adaptor NlpI in complex with the endopeptidase MepS, revealing atomic details of how NlpI recruits multiple MepS molecules and subsequently influences PG expansion. NlpI binding elicits a disorder-to-order transition in the intrinsically disordered N-terminal of MepS, concomitantly promoting the dimerization of monomeric MepS. This results in the alignment of two asymmetric MepS dimers respectively located on the two opposite sides of the dimerization interface of NlpI, thus enhancing MepS activity in PG hydrolysis. Notably, the protein level of MepS is primarily modulated by the tail-specific protease Prc, which is known to interact with NlpI. The structure of the Prc-NlpI-MepS complex demonstrates that NlpI brings together MepS and Prc, leading to the efficient MepS degradation by Prc. Collectively, our results provide structural insights into the NlpI-enabled avidity effect of cellular endopeptidases and NlpI-directed MepS degradation by Prc.

Date: 2024
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DOI: 10.1038/s41467-024-49552-y

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