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Structure paper

TitleStructural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis.
Journal, issue, pagesEMBO J, Vol. 41, Issue 13, Page e109755, Year 2022
Publish dateJul 4, 2022
AuthorsLeehyeon Kim / Byung-Gil Lee / Minki Kim / Min Kyung Kim / Do Hoon Kwon / Hyunmin Kim / Heike Brötz-Oesterhelt / Soung-Hun Roh / Hyun Kyu Song /
PubMed AbstractThe ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. ...The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease.
External linksEMBO J / PubMed:35593068 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.79 - 3.4 Å
Structure data

31559

7fep

EMDB-31559, PDB-7fep:
Cryo-EM structure of BsClpP-ADEP1 complex at pH 6.5
Method: EM (single particle) / Resolution: 3.1 Å

31560

7feq

EMDB-31560, PDB-7feq:
Cryo-EM structure of apo BsClpP at pH 6.5
Method: EM (single particle) / Resolution: 3.2 Å

31561

7fer

EMDB-31561, PDB-7fer:
Cryo-EM structure of BsClpP-ADEP1 complex at pH 4.2
Method: EM (single particle) / Resolution: 3.4 Å

31562

7fes

EMDB-31562, PDB-7fes:
Cryo-EM structure of apo BsClpP at pH 4.2
Method: EM (single particle) / Resolution: 3.4 Å

PDB-7p80:
Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compressed state)
Method: X-RAY DIFFRACTION / Resolution: 2.98 Å

PDB-7p81:
Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compact state)
Method: X-RAY DIFFRACTION / Resolution: 2.79 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • bacillus subtilis (bacteria)
  • synthetic construct (others)
  • bacillus subtilis (strain 168) (bacteria)
KeywordsHYDROLASE / ClpP / Bacillus subtilis / ADEP1 / Acyldepsipeptides / ADEP2 / compressed / antibiotics

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