3KTI

Structure of ClpP in complex with ADEP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 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, 3KTH, 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 elusive because of the lack of a complex structure ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G
A, B, C, D, E, F, G
199Bacillus subtilisMutation(s): 0 
Gene Names: clpPyvdNBSU34540
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
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acyldepsipeptide 1
H, I, J, K, L, M, N
H, I, J, K, L, M, N
7N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MAA
Query on MAA
H, I, J, K, L, M, N
H, I, J, K, L, M, N
L-PEPTIDE LINKINGC4 H9 N O2ALA
MP8
Query on MP8
H, I, J, K, L, M, N
H, I, J, K, L, M, N
L-PEPTIDE LINKINGC6 H11 N O2PRO
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000503
Query on PRD_000503
H, I, J, K, L, M, NADEP1Cyclic depsipeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.645α = 90
b = 151.756β = 120.03
c = 100.665γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Other