3KTH

Structure of ClpP from Bacillus subtilis in orthorombic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism

Lee, B.-G.Park, E.Y.Lee, K.-E.Jeon, H.Sung, K.H.Paulsen, H.Rubsamen-Schaeff, H.Brotz-Oesterhelt, H.Song, H.K.

(2010) Nat.Struct.Mol.Biol. 17: 471-478

  • DOI: 10.1038/nsmb.1787
  • Primary Citation of Related Structures:  3KTG, 3KTI, 3KTJ, 3KTK

  • PubMed Abstract: 
  • Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. Nonetheless, the proteolytic activation mechanism has remained ...

    Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. Nonetheless, the proteolytic activation mechanism has remained elusive because of the lack of a complex structure. Acyldepsipeptides (ADEPs), a recently discovered class of antibiotics, activate and disregulate ClpP. Here we have elucidated the structural changes underlying the ClpP activation process by ADEPs. We present the structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2. The structures show the closed-to-open-gate transition of the ClpP N-terminal segments upon activation as well as conformational changes restricted to the upper portion of ClpP. The direction of the conformational movement and the hydrophobic clustering that stabilizes the closed structure are markedly different from those of other ATP-dependent proteases, providing unprecedented insights into the activation of ClpP.


    Organizational Affiliation

    School of Life Sciences and Biotechnology, Korea University, Seoul, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G
199Bacillus subtilis (strain 168)Gene Names: clpP (yvdN)
EC: 3.4.21.92
Find proteins for P80244 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P80244
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.293α = 90.00
b = 108.117β = 90.00
c = 152.644γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance