Phage lysis protein LysM acts as a wedge to block MurJ conformational changes

Kohga, H.; Lertpreedakorn, N.; Miyazaki, R.; Wu, S.; Tanaka, H.; Takahashi, Y. S.; Hosoda, K.; Yoshikaie, K.; Kuruma, Y.; Shigematsu, H.; Mori, T.; Tsukazaki, T.

doi:10.1101/2025.04.26.650401

bioRxiv · 10.1101/2025.04.26.650401

Phage lysis protein LysM acts as a wedge to block MurJ conformational changes

Kohga, H.·Lertpreedakorn, N.·Miyazaki, R.·Wu, S.·Tanaka, H.·Takahashi, Y. S.·Hosoda, K.·Yoshikaie, K.·Kuruma, Y.·Shigematsu, H.·Mori, T.·Tsukazaki, T.

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Abstract

Many antibiotics target essential cellular processes. To combat multidrug-resistant bacteria, new antibacterial strategies are needed. In the peptidoglycan biogenesis pathway in Escherichia coli, MurJ, the lipid II flippase, is an essential membrane protein. The 37-residue protein M from the Levivirus phage, known as LysM or SglM, targets MurJ and induces cell lysis; however, its molecular mechanism remains unclear. Here, we present the cryo-EM structure of the MurJ/LysM (JM) complex at 3.09 [A] resolution, revealing that LysM interacts with the crevasse between TM2 and TM7 of MurJ, locking MurJ in an outward-facing conformation, with LysM acting like a wedge. Alanine-scanning mutagenesis and pull-down assays revealed key residues responsible for LysM function, and molecular dynamics simulations showed that LysM stabilizes MurJs outward-facing state. These findings demonstrate an unprecedented phage-derived mechanism for blocking lipid II transport, providing a structural framework for designing MurJ-targeted antimicrobial agents.

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Kohga, H., Lertpreedakorn, N., Miyazaki, R., Wu, S., Tanaka, H., Takahashi, Y. S., Hosoda, K., Yoshikaie, K., Kuruma, Y., Shigematsu, H., Mori, T., Tsukazaki, T.. 2025-04-26. Phage lysis protein LysM acts as a wedge to block MurJ conformational changes. https://doi.org/10.1101/2025.04.26.650401

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