3MT6

Structure of ClpP from Escherichia coli in complex with ADEP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    3MT6

  • 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 acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit207Escherichia coli K-12Mutation(s): 0 
Gene Names: b0437clpPJW0427lopP
EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12))
Explore P0A6G7 
Go to UniProtKB:  P0A6G7
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACYLDEPSIPEPTIDE 17Streptomyces hawaiiensisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AC [auth V] , AD [auth C] , BC [auth W] , BD [auth B] , CC [auth W] , CD [auth B] , DC [auth X] , DD [auth A] , 
AC [auth V], AD [auth C], BC [auth W], BD [auth B], CC [auth W], CD [auth B], DC [auth X], DD [auth A], EB [auth R], EC [auth X], ED [auth A], FB [auth R], FC [auth M], FD [auth G], GB [auth R], GC [auth M], GD [auth G], HB [auth S], HC [auth M], IB [auth T], IC [auth L], JB [auth T], JC [auth L], KB [auth U], KC [auth K], LB [auth U], LC [auth K], MB [auth O], MC [auth J], NB [auth O], NC [auth J], OB [auth P], OC [auth I], PB [auth P], PC [auth I], QB [auth Q], QC [auth H], RB [auth Q], RC [auth N], SB [auth Y], SC [auth N], TB [auth Z], TC [auth F], UB [auth Z], UC [auth E], VB [auth Z], VC [auth E], WB [auth a], WC [auth E], XB [auth b], XC [auth D], YB [auth b], YC [auth D], ZB [auth V], ZC [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MAA
Query on MAA
AB [auth z] , BB [auth 3] , CA [auth 1] , CB [auth 4] , DA [auth 2] , DB [auth u] , EA [auth c] , FA [auth d] , 
AB [auth z],  BB [auth 3],  CA [auth 1],  CB [auth 4],  DA [auth 2],  DB [auth u],  EA [auth c],  FA [auth d],  GA [auth e],  HA [auth f],  IA [auth g],  JA [auth h],  KA [auth i],  LA [auth j],  MA [auth k],  NA [auth l],  OA [auth m],  PA [auth n],  QA [auth o],  RA [auth p],  SA [auth q],  TA [auth r],  UA [auth s],  VA [auth t],  WA [auth v],  XA [auth w],  YA [auth x],  ZA [auth y]
L-PEPTIDE LINKINGC4 H9 N O2ALA
MP8
Query on MP8
AB [auth z] , BB [auth 3] , CA [auth 1] , CB [auth 4] , DA [auth 2] , DB [auth u] , EA [auth c] , FA [auth d] , 
AB [auth z],  BB [auth 3],  CA [auth 1],  CB [auth 4],  DA [auth 2],  DB [auth u],  EA [auth c],  FA [auth d],  GA [auth e],  HA [auth f],  IA [auth g],  JA [auth h],  KA [auth i],  LA [auth j],  MA [auth k],  NA [auth l],  OA [auth m],  PA [auth n],  QA [auth o],  RA [auth p],  SA [auth q],  TA [auth r],  UA [auth s],  VA [auth t],  WA [auth v],  XA [auth w],  YA [auth x],  ZA [auth y]
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
AB [auth 1], BB [auth 2], CA [auth 3], CB [auth 4], DA [auth c], DB [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]ADEP1Cyclic depsipeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.254α = 90
b = 121.15β = 91.38
c = 276.17γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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