8OTK | pdb_00008otk

Structure of ClpC Q11P N-terminal Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

MdfA is a novel ClpC adaptor protein that functions in the developing Bacillus subtilis spore.

Massoni, S.C.Evans, N.J.Hantke, I.Fenton, C.Torpey, J.H.Collins, K.M.Krysztofinska, E.M.Muench, J.H.Thapaliya, A.Martinez-Lumbreras, S.Hart Ferrell, S.Slater, C.Wang, X.Fekade, R.Obwar, S.Yin, S.Vazquez, A.Prior, C.B.Turgay, K.Isaacson, R.L.Camp, A.H.

(2025) Genes Dev 39: 510-523

  • DOI: https://doi.org/10.1101/gad.352498.124
  • Primary Citation of Related Structures:  
    8OTK

  • PubMed Abstract: 

    Bacterial protein degradation machinery consists of chaperone-protease complexes that play vital roles in bacterial growth and development and have sparked interest as novel antimicrobial targets. ClpC-ClpP (ClpCP) is one such chaperone-protease complex, recruited by adaptors to specific functions in the model bacterium Bacillus subtilis and other Gram-positive bacteria, including the pathogens Staphylococcus aureus and Mycobacterium tuberculosis Here we have identified a new ClpCP adaptor protein, MdfA (metabolic differentiation factor A; formerly YjbA), in a genetic screen for factors that help drive B. subtilis toward metabolic dormancy during spore formation. A knockout of mdfA stimulates gene expression in the developing spore, while aberrant expression of mdfA during vegetative growth is toxic. MdfA binds directly to ClpC to induce its oligomerization and ATPase activity, and this interaction is required for the in vivo effects of mdfA Finally, a cocrystal structure reveals that MdfA binds to the ClpC N-terminal domain at a location analogous to that on the M. tuberculosis ClpC1 protein where bactericidal cyclic peptides bind. Altogether, our data and that of an accompanying study by Riley and colleagues support a model in which MdfA induces ClpCP-mediated degradation of metabolic enzymes in the developing spore, helping drive it toward metabolic dormancy.


  • Organizational Affiliation
    • Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpC / Negative regulator of tic competence clcC/mecB155Bacillus subtilisMutation(s): 0 
Gene Names: B4417_1475
UniProt
Find proteins for P37571 (Bacillus subtilis (strain 168))
Explore P37571 
Go to UniProtKB:  P37571
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37571
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
G [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.621α = 90
b = 84.621β = 90
c = 32.16γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references, Structure summary