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TitleComprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization.
Journal, issue, pagesPLoS Biol, Vol. 21, Issue 2, Page e3001987, Year 2023
Publish dateFeb 6, 2023
AuthorsDamu Wu / Yan Liu / Yuhao Dai / Guopeng Wang / Guoliang Lu / Yan Chen / Ningning Li / Jinzhong Lin / Ning Gao /
PubMed AbstractThe human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of- ...The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.
External linksPLoS Biol / PubMed:36745679 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.1 - 7.5 Å
Structure data

33104

7xbk

EMDB-33104, PDB-7xbk:
Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-33105: Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB
Method: EM (single particle) / Resolution: 6.8 Å

EMDB-33106: Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB
Method: EM (single particle) / Resolution: 7.5 Å

EMDB-33109: Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB
Method: EM (single particle) / Resolution: 7.4 Å

EMDB-33110: Cry-EM structure of CLPB NBD organized in heptamer
Method: EM (single particle) / Resolution: 4.1 Å

PDB-7xc5:
Crystal structure of the ANK domain of CLPB
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsCHAPERONE / CLPB / AAA-ATPase / HYDROLASE / ANK repeat / TRANSPORT PROTEIN

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