3MT6 | pdb_00003mt6

Structure of ClpP from Escherichia coli in complex with ADEP1

• PDB DOI: https://doi.org/10.2210/pdb3MT6/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Escherichia coli K-12, Streptomyces hawaiiensis
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

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

• PubMed: 20851345 
• DOI: https://doi.org/10.1016/j.chembiol.2010.07.008
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.

Biological Assembly 1  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Hetero 28-mer - A14B14 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 28-mer - A14B1C1D1E1F1G1H1I1J1K1L1M1N1O1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Hetero 28-mer - A14B14 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 28-mer - A14B1C1D1E1F1G1H1I1J1K1L1M1N1O1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 677.09 kDa 
• Atom Count: 46,463 
• Modeled Residue Count: 5,428 
• Deposited Residue Count: 5,992 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A [auth R], AA [auth A], B [auth S], BA [auth G], C [auth T], D [auth U], E [auth O], F [auth P], G [auth Q], H [auth Y], I [auth Z], J [auth a], K [auth b], L [auth V], M [auth W], N [auth X], O [auth M], P [auth L], Q [auth K], R [auth J], S [auth I], T [auth H], U [auth N], V [auth F], W [auth E], X [auth D], Y [auth C], Z [auth B]	207	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0437, clpP, JW0427, lopP EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7  Go to UniProtKB:  P0A6G7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYLDEPSIPEPTIDE 1	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]	7	Streptomyces hawaiiensis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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], 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 LINKING	C4 H9 N O2		ALA
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], 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 LINKING	C6 H11 N O2		PRO

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
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]	ADEP1	Cyclic depsipeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.254	α = 90
b = 121.15	β = 91.38
c = 276.17	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2016-03-30
  Changes: Non-polymer description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection