7FES

Cryo-EM structure of apo BsClpP at pH 4.2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis.

Kim, L.Lee, B.G.Kim, M.Kim, M.K.Kwon, D.H.Kim, H.Brotz-Oesterhelt, H.Roh, S.H.Song, H.K.

(2022) EMBO J 41: e109755-e109755

  • DOI: https://doi.org/10.15252/embj.2021109755
  • Primary Citation of Related Structures:  
    7FEP, 7FEQ, 7FER, 7FES, 7P80, 7P81

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Life Sciences, Korea University, Seoul, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
202Bacillus subtilisMutation(s): 0 
EC: 3.4.21.92
UniProt
Find proteins for P80244 (Bacillus subtilis (strain 168))
Explore P80244 
Go to UniProtKB:  P80244
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80244
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2020R1A2C3008285
National Research Foundation (NRF, Korea)Korea, Republic Of2020R1A5A1019023
National Research Foundation (NRF, Korea)Korea, Republic Of2021M3A9I4030068
National Research Foundation (NRF, Korea)Korea, Republic Of2021M3A9I4021220
National Research Foundation (NRF, Korea)Korea, Republic Of2019M3E5D6063871
National Research Foundation (NRF, Korea)Korea, Republic Of2020R1A5A1018081

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Data collection