9dqk

From Proteopedia

human ClpP - Apo - A192E / E196R

Structural highlights

9dqk is a 14 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.75Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLPP_HUMAN Clp cleaves peptides in various proteins in a process that requires ATP hydrolysis. Clp may be responsible for a fairly general and central housekeeping function rather than for the degradation of specific substrates.

Publication Abstract from PubMed

Human ClpP protease contributes to mitochondrial protein quality control by degrading misfolded proteins. ClpP is overexpressed in cancers such as acute myeloid leukemia (AML), where its inhibition leads to the accumulation of damaged respiratory chain subunits and cell death. Conversely, hyperactivating ClpP with small-molecule activators, such as the recently discovered ONC201, disrupts mitochondrial protein degradation and impairs respiration in cancer cells. Despite its critical role in human health, the mechanism underlying the structural and functional properties of human ClpP remains elusive. Notably, human ClpP is paradoxically activated by active-site inhibitors. All available structures of human ClpP published to date are in the inactive compact or compressed states, surprisingly even when ClpP is bound to an activator molecule such as ONC201. Here, we present structures of human mitochondrial ClpP in the active extended state, including a pair of structures where ClpP is bound to an active-site inhibitor. We demonstrate that amino acid substitutions in the handle region (A192E and E196R) recreate a conserved salt bridge found in bacterial ClpP, stabilizing the extended active state and significantly enhancing ClpP activity. We elucidate the ClpP activation mechanism, highlighting a hormetic effect where substoichiometric inhibitor binding triggers an allosteric transition that drives ClpP into its active extended state. Our findings link the conformational dynamics of ClpP to its catalytic function and provide high-resolution structures for the rational design of potent and specific ClpP inhibitors, with implications for targeting AML and other disorders with ClpP involvement.

Mechanism of allosteric activation in human mitochondrial ClpP protease.,Goncalves MM, Uday AB, Forrester TJB, Currie SQW, Kim AS, Feng Y, Jitkova Y, Velyvis A, Harkness RW, Kimber MS, Schimmer AD, Zeytuni N, Vahidi S Proc Natl Acad Sci U S A. 2025 Apr 22;122(16):e2419881122. doi: , 10.1073/pnas.2419881122. Epub 2025 Apr 15. PMID:40232800^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Goncalves MM, Uday AB, Forrester TJB, Currie SQW, Kim AS, Feng Y, Jitkova Y, Velyvis A, Harkness RW, Kimber MS, Schimmer AD, Zeytuni N, Vahidi S. Mechanism of allosteric activation in human mitochondrial ClpP protease. Proc Natl Acad Sci U S A. 2025 Apr 22;122(16):e2419881122. PMID:40232800 doi:10.1073/pnas.2419881122