Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 43; pp. E4587 - E4595
• Main Authors: Schmitz, Karl R, Carney, Daniel W, Sello, Jason K, Sauer, Robert T
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 28-10-2014; National Acad Sciences
• Series: PNAS Plus
• Subjects: Adenosine triphosphatase; Adenosine Triphosphatases - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding sites; Biological Sciences; Catalytic Domain; Crystallography, X-Ray; Enzyme Activation; Enzyme Stability; Enzymes; Gram-positive bacteria; Models, Biological; Mycobacterium tuberculosis; Mycobacterium tuberculosis - enzymology; Peptide Hydrolases - metabolism; Peptides; Peptides, Cyclic - chemistry; Peptides, Cyclic - metabolism; PNAS Plus; Protein Binding; Protein Multimerization; Protein Subunits - chemistry; Protein Subunits - metabolism; Substrate Specificity; pathogen drug target; AAA+ proteases; allosteric coupling
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1417120111

Significance Caseinolytic peptidase P (ClpP) normally collaborates with ATPases associated with diverse activities (AAA+) partner proteins, such as ClpX and ClpC, to carry out energy-dependent degradation of proteins within cells. The ClpP enzyme from Mycobacterium tuberculosis is required for survival of this human pathogen, is a validated drug target, and is unusual in consisting of discrete ClpP1 and ClpP2 rings. We solved the crystal structure of ClpP1P2 bound to peptides that mimic binding of protein substrates and small molecules that mimic binding of a AAA+ partner and cause unregulated rogue proteolysis. These studies explain why two different ClpP rings are required for peptidase activity and provide a foundation for the rational development of drugs that target ClpP1P2 and kill M. tuberculosis .
Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into catalytically active homo-tetradecamers able to cleave small peptides, the Mycobacterium tuberculosis enzyme consists of discrete ClpP1 and ClpP2 heptamers that require a AAA+ partner and protein–substrate delivery or a peptide agonist to stabilize assembly of the active tetradecamer. Here, we show that cyclic acyldepsipeptides (ADEPs) and agonist peptides synergistically activate ClpP1P2 by mimicking AAA+ partners and substrates, respectively, and determine the structure of the activated complex. Our studies establish the basis of heteromeric ClpP1P2 assembly and function, reveal tight coupling between the conformations of each ring, show that ADEPs bind only to one ring but appear to open the axial pores of both rings, provide a foundation for rational drug development, and suggest strategies for studying the roles of individual ClpP1 and ClpP2 rings in Clp-family proteolysis.