8P66 | pdb_00008p66

Structural basis of aggregate binding/recognition by the AAA+ disaggregase ClpG

• PDB DOI: https://doi.org/10.2210/pdb8P66/pdb
• BMRB: 34818

• Classification: CHAPERONE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-25 Released: 2023-11-01 
• Deposition Author(s): Simon, B., Hennig, J., Mogk, A.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structural basis of aggregate binding by the AAA+ disaggregase ClpG.

Katikaridis, P., Simon, B., Jenne, T., Moon, S., Lee, C., Hennig, J., Mogk, A.

(2023) J Biological Chem 299: 105336-105336

• PubMed: 37827289 
• DOI: https://doi.org/10.1016/j.jbc.2023.105336
• Primary Citation Related Structures: 
  8P66


• PubMed Abstract: 
  

  Severe heat stress causes massive loss of essential proteins by aggregation, necessitating a cellular activity that rescues aggregated proteins. This activity is executed by ATP-dependent, ring-forming, hexameric AAA+ disaggregases. Little is known about the recognition principles of stress-induced protein aggregates. How can disaggregases specifically target aggregated proteins, while avoiding binding to soluble non-native proteins? Here, we determined by NMR spectroscopy the core structure of the aggregate-targeting N1 domain of the bacterial AAA+ disaggregase ClpG, which confers extreme heat resistance to bacteria. N1 harbors a Zn ²⁺ -coordination site that is crucial for structural integrity and disaggregase functionality. We found that conserved hydrophobic N1 residues located on a β-strand are crucial for aggregate targeting and disaggregation activity. Analysis of mixed hexamers consisting of full-length and N1-truncated subunits revealed that a minimal number of four N1 domains must be present in a AAA+ ring for high-disaggregation activity. We suggest that multiple N1 domains increase substrate affinity through avidity effects. These findings define the recognition principle of a protein aggregate by a disaggregase, involving simultaneous contacts with multiple hydrophobic substrate patches located in close vicinity on an aggregate surface. This binding mode ensures selectivity for aggregated proteins while sparing soluble, non-native protein structures from disaggregase activity.

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Organizational Affiliation: 
• Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany; Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
Department of Biological Sciences, Ajou University, Suwon, South Korea.
Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany; Division of Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany. Electronic address: [e-mail].
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content 

• Total Structure Weight: 6.46 kDa 
• Atom Count: 446 
• Modeled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clp protease ClpC,Heat shock survival AAA family ATPase ClpK	A [auth B]	54	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: BI380_06745, clpK
UniProt
Find proteins for A0A7M2ZW85 (Pseudomonas aeruginosa) Explore A0A7M2ZW85  Go to UniProtKB:  A0A7M2ZW85

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Simon, B., Hennig, J., Mogk, A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	MO970/7-1

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Database references