RT Journal Article SR Electronic T1 Opening the side exit pores of ClpP by lowering the pH of proteolytic chamber coupled with substrate hydrolysis JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.09.20.461017 DO 10.1101/2021.09.20.461017 A1 Leehyeon Kim A1 Byung-Gil Lee A1 Min Kyung Kim A1 Do Hoon Kwon A1 Hyunmin Kim A1 Heike Brötz-Oesterhelt A1 Soung-Hun Roh A1 Hyun Kyu Song YR 2021 UL http://biorxiv.org/content/early/2021/09/21/2021.09.20.461017.abstract AB The ClpP serine peptidase is a tetradecameric degradation machine involved in many physiological processes. It becomes a competent ATP-dependent protease with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause dysregulation and activation of ClpP without ATPases, and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed the structural details, conformational changes, and activation mechanism. Although product release by the side exit pores has been proposed, the detailed driving force for product release remains elusive. Here, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures revealed various conformational states at different pH conditions. To understand the conformational change for product release, we investigated the relationship between substrate hydrolysis and the pH lowering process. Our data, together with previous findings, provide insight into the molecular mechanism of product release by ClpP self-compartmentalizing protease.