Molecular basis for zymogen-like autoinhibition of the M60-like metallopeptidase YghJ

YghJ is a PF13402-family M60-like metallopeptidase secreted by pathogenic Escherichia coli and implicated in mucin degradation. Here, we determined cryo-electron microscopy structures of YghJ at approximately 3.0 Å, revealing a full-length zymogen-like autoinhibited state (YghJZ) and an N-terminally processed, substrate-accessible state (YghJSA). In YghJZ, the N-terminal LBD–IGD1 region clamps the M60-like domain, occludes the substrate-access channel, and contributes His236 as an additional ligand to the catalytic Zn2+ center. In YghJSA, this restraint is absent, the catalytic center is solvent-exposed, and the Zn2+ site adopts a canonical configuration. The two states also differ in global domain organization, with rearrangement of the Met910–Leu916 loop in the linker domain accompanying active-site exposure. Processed YghJ species were detected in chromosomally Flag-tagged E. coli MG1655, indicating that processing is not restricted to recombinant purification. Although purified YghJ showed no unambiguous cleavage of the tested mucin substrates, these structures support a zymogen-like autoinhibition model and provide a framework for understanding the processing-associated regulation of YghJ.