3MT6

Structure of ClpP from Escherichia coli in complex with ADEP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.

Li, D.H.Chung, Y.S.Gloyd, M.Joseph, E.Ghirlando, R.Wright, G.D.Cheng, Y.Q.Maurizi, M.R.Guarne, A.Ortega, J.

(2010) Chem.Biol. 17: 959-969

  • DOI: 10.1016/j.chembiol.2010.07.008
  • Also Cited By: 6CFD, 5W18, 5VZ2

  • PubMed Abstract: 
  • In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acy ...

    In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli ClpP bound to ADEP1 and report the structural changes underlying ClpP activation. ADEP1 binds in the hydrophobic groove that serves as the primary docking site for ClpP ATPases. Binding of ADEP1 locks the N-terminal loops of ClpP in a β-hairpin conformation, generating a stable pore through which extended polypeptides can be threaded. This structure serves as a model for ClpP in the holoenzyme ClpAP and ClpXP complexes and provides critical information to further develop this class of antibiotics.


    Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
R, S, T, U, O, P, Q, Y, Z, a, b, V, W, X, M, L, K, J, I, H, N, F, E, D, C, B, A, G
207Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: clpP (lopP)
EC: 3.4.21.92
Find proteins for P0A6G7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6G7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACYLDEPSIPEPTIDE 1
1, 2, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, v, w, x, y, z, 3, 4, u
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
a, A, B, b, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000503
Query on PRD_000503
1,2,3,4,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,y,zADEP1Cyclic depsipeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.254α = 90.00
b = 121.150β = 91.38
c = 276.170γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-30 
  • Released Date: 2010-11-03 
  • Deposition Author(s): Chung, Y.S.

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2016-03-30
    Type: Non-polymer description