Molecular Playground/ClpP

ClpP Introduction

E. coli Casein lytic proteinase P (ClpP) is a double ring tetradecameric homo oligomer compartmentalized peptidase [1]. ClpP requires the use of ATP dependent regulatory elements that independently bind to ClpP in order for substrates to have access the active core [2][3][4]. Here, proteins that are translocated by regulatory elements into the peptidase core are cleaved into smaller amino acid chains approximately on average 6-8aa in length [5].

Tetradecameric Structure

ClpP is a serine protease which consists of fourteen monomers situated into two heptameric rings seated on top of each other. In the center of the barrel-shaped chamber lies a core of fourteen peptide-cleaving active sites, restricted by the narrow entrance called the . As peptides are processively threaded in the pore by the regulatory elements, the peptides are then degraded into smaller fragments as a result from ClpP cleavage. Smaller peptides are then released through small openings found around the of the two stacked rings.

Structural highlights

Featured within the core of ClpP are the catalytic sets of amino acids [] that constitute the active mechanism featured by serene proteases [6][7]. Human ClpP can exist in two forms, a single heptameric ring or as a double stack set of hepatmeric rings where the double stacked form (tetradecamer) is the active form [8]. Tetradecamer ClpP is a stable but not a rigid structure that can undergo several conformational forms when interacting with its regulatory elements. By doing so both stabilizes processivity of translocation by the regulatory elements and is thought to increase likelihood of exposure to the active sites resulting in timely, small peptide formation.

Role of ClpP/Biological Relevance

E. coli ClpAP/ClpXP complexes play a critical role in maintaining protein homeostasis under several levels of quality control. Improperly folded or aggregated proteins are potential ClpP substrates based on properties of the associated regulatory element recognition. Targeted removal of aberrant proteins resulting from and rescue of stalled ribosomes by the SsrA tagging system are directly recognized and degraded by ClpAP/ClpXP complexes [9]. In E. coli ClpP and ClpP homologues found in other bacteria require regulatory elements to recognize and import proteins for destruction. To gain access to the active sites is tightly controlled and therefore a potential antimicrobial target where loss of regulation (for example, through use of acyldepsipeptides or ADEPs) literally digests the bacteria from the inside out [10]. E. coli ClpAP and ClpXP has been used as a structural model for the 26 proteasome to gain insight into its workings [11][12].

References

1. ClpP: A structurally dynamic protease regulated by AAA+ proteins. Alexopoulos JA et. al (2012 J Struct Bio)

2. ClpA and ClpX ATPases bind simultaneously to opposite ends of ClpP peptidase to form active hybrid complexes. Ortega J et. al (2004 J. Struct Biol.)

3. Binding of the ClpA Unfoldase Opens the Axial Gate of ClpP Peptidase. Effantin et. al (2010 J Biol Chem)

4. Turned on for degradation: ATPase-independent degradation by ClpP. Bewley MC et. al (2009 J Struct Biol)

5. Control of peptide product sizes by the energy-dependent protease ClpAP. Choi KH et. al (2005 Biochemistry)

6. Clp P represents a unique family of serine proteases. Maurizi MR et. al (1990 J Biolchem)

7. ClpP: a distinctive family of cylindrical energy-dependent serine proteases. Yu AY et. al (2007 FEBS Lett.)

8. Human mitochondrial ClpP is a stable heptamer that assembles into a tetradecamer in the presence of ClpX. Kang SG et. al (2007 J Biol Chem)

9. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Gottesman S et. al (1998 Genes Dev.)

10. Bacterial Cell Stress Protein ClpP: A Novel Antibiotic Target. Brötz-Oesterhelt et. al (2013 Heat Shock Proteins Volume 7, pp 375-385)

11. Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome. Kessel M et. al (1995 J Mol Bio)

12. Proteasomes and their kin: proteases in the machine age. Pickart CM et. al (2004 Nat Rev Mol Cell Biol.)

Acknowledgements

Kamal Joshi, Joanne Lau, Jing Liu, Rob Vass, Lisa Hernandez

PDB id:1YG6 from Bewley, MC et. al (2006 J.Struct.Biol.)