6PKA

Structure of ClpP from Staphylococcus aureus in complex with ureadepsipeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ureadepsipeptides as ClpP Activators.

Griffith, E.C.Zhao, Y.Singh, A.P.Conlon, B.P.Tangallapally, R.Shadrick, W.R.Liu, J.Wallace, M.J.Yang, L.Elmore, J.M.Li, Y.Zheng, Z.Miller, D.J.Cheramie, M.N.Lee, R.B.LaFleur, M.D.Lewis, K.Lee, R.E.

(2019) ACS Infect Dis 5: 1915-1925

  • DOI: 10.1021/acsinfecdis.9b00245
  • Primary Citation of Related Structures:  
    5VZ2, 5W18, 6PKA, 6PMD

  • PubMed Abstract: 
  • Acyldepsipeptides are a unique class of antibiotics that act via allosterically dysregulated activation of the bacterial caseinolytic protease (ClpP). The ability of ClpP activators to kill nongrowing bacteria represents a new opportunity to combat deep-seated biofilm infections ...

    Acyldepsipeptides are a unique class of antibiotics that act via allosterically dysregulated activation of the bacterial caseinolytic protease (ClpP). The ability of ClpP activators to kill nongrowing bacteria represents a new opportunity to combat deep-seated biofilm infections. However, the acyldepsipeptide scaffold is subject to rapid metabolism. Herein, we explore alteration of the potentially metabolically reactive α,β unsaturated acyl chain. Through targeted synthesis, a new class of phenyl urea substituted depsipeptide ClpP activators with improved metabolic stability is described. The ureadepsipeptides are potent activators of Staphylococcus aureus ClpP and show activity against Gram-positive bacteria, including S. aureus biofilms. These studies demonstrate that a phenyl urea motif can successfully mimic the double bond, maintaining potency equivalent to acyldepsipeptides but with decreased metabolic liability. Although removal of the double bond from acyldepsipeptides generally has a significant negative impact on potency, structural studies revealed that the phenyl ureadepsipeptides can retain potency through the formation of a third hydrogen bond between the urea and the key Tyr63 residue in the ClpP activation domain. Ureadepsipeptides represent a new class of ClpP activators with improved drug-like properties, potent antibacterial activity, and the tractability to be further optimized.


    Organizational Affiliation

    Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , 262 Danny Thomas Place , Memphis , Tennessee 38105 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G, H [auth I]
203Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: clpPSAOUHSC_00790
EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G036 
Go to UniProtKB:  Q2G036
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide7synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MP8
Query on MP8
AA [auth b] , BA [auth c] , O [auth H] , P [auth J] , Q [auth O] , R [auth P] , S [auth Q] , T [auth R] , 
AA [auth b],  BA [auth c],  O [auth H],  P [auth J],  Q [auth O],  R [auth P],  S [auth Q],  T [auth R],  U,  V,  W [auth X],  X [auth Y],  Y [auth Z],  Z [auth a]
L-PEPTIDE LINKINGC6 H11 N O2PRO
WFP
Query on WFP
AA [auth b] , BA [auth c] , O [auth H] , P [auth J] , Q [auth O] , R [auth P] , S [auth Q] , T [auth R] , 
AA [auth b],  BA [auth c],  O [auth H],  P [auth J],  Q [auth O],  R [auth P],  S [auth Q],  T [auth R],  U,  V,  W [auth X],  X [auth Y],  Y [auth Z],  Z [auth a]
L-PEPTIDE LINKINGC9 H9 F2 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002359
Query on PRD_002359
AA [auth H], BA [auth J], O, P, Q, R, S [auth U], T [auth V], U [auth X], V [auth Y], W [auth Z], X [auth a], Y [auth b], Z [auth c]OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptideOligopeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.957α = 90
b = 126.681β = 93.36
c = 146.776γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI110578

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence