7AA4

Structure of ClpC1-NTD bound to a CymA analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

BacPROTACs mediate targeted protein degradation in bacteria.

Morreale, F.E.Kleine, S.Leodolter, J.Junker, S.Hoi, D.M.Ovchinnikov, S.Okun, A.Kley, J.Kurzbauer, R.Junk, L.Guha, S.Podlesainski, D.Kazmaier, U.Boehmelt, G.Weinstabl, H.Rumpel, K.Schmiedel, V.M.Hartl, M.Haselbach, D.Meinhart, A.Kaiser, M.Clausen, T.

(2022) Cell 185: 2338

  • DOI: 10.1016/j.cell.2022.05.009
  • Primary Citation of Related Structures:  
    7AA4, 7ABR

  • PubMed Abstract: 
  • Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis-targeting chimeras. Despite their great promise for medical chemistry, so far, it has not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections ...

    Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis-targeting chimeras. Despite their great promise for medical chemistry, so far, it has not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections. Here, we develop small-molecule degraders, so-called BacPROTACs, that bind to the substrate receptor of the ClpC:ClpP protease, priming neo-substrates for degradation. In addition to their targeting function, BacPROTACs activate ClpC, transforming the resting unfoldase into its functional state. The induced higher-order oligomer was visualized by cryo-EM analysis, providing a structural snapshot of activated ClpC unfolding a protein substrate. Finally, drug susceptibility and degradation assays performed in mycobacteria demonstrate in vivo activity of BacPROTACs, allowing selective targeting of endogenous proteins via fusion to an established degron. In addition to guiding antibiotic discovery, the BacPROTAC technology presents a versatile research tool enabling the inducible degradation of bacterial proteins.


    Organizational Affiliation

    Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria; Medical University of Vienna, 1030 Vienna, Austria. Electronic address: tim.clausen@imp.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Negative regulator of genetic competence ClpC/mecBA156Mycobacterium tuberculosisMutation(s): 0 
Gene Names: clpC_1ERS007741_03095
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPC9 
Go to UniProtKB:  P9WPC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPC9
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
polymer Cyclomarin A analogueB7StreptomycesMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLE
Query on MLE
B L-PEPTIDE LINKINGC7 H15 N O2LEU
WPA
Query on WPA
B L-PEPTIDE LINKINGC10 H13 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.35α = 86.18
b = 33.68β = 94.22
c = 35.81γ = 103.18
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Vienna Science and Technology Fund (WWTF)AustriaWWTF // LS17-29

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references