Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis

The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli C...

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Bibliographic Details
Published in:	Nature structural & molecular biology Vol. 27; no. 5; pp. 406 - 416
Main Authors:	Lopez, Kyle E., Rizo, Alexandrea N., Tse, Eric, Lin, JiaBei, Scull, Nathaniel W., Thwin, Aye C., Lucius, Aaron L., Shorter, James, Southworth, Daniel R.
Format:	Journal Article
Language:	English
Published:	New York Nature Publishing Group US 01-05-2020 Nature Publishing Group
Subjects:	101/28 631/45/468 631/45/470/1981 631/535/1258/1259 82/16 82/83 Adenosine Triphosphate - analogs & derivatives Adenosine Triphosphate - metabolism Biochemistry Biodegradation Biological Microscopy Biomedical and Life Sciences Cryoelectron Microscopy DNA Helicases - metabolism E coli Endopeptidase Clp - chemistry Endopeptidase Clp - genetics Endopeptidase Clp - metabolism Escherichia coli Escherichia coli - chemistry Escherichia coli - genetics Escherichia coli - metabolism Escherichia coli Proteins - chemistry Escherichia coli Proteins - genetics Escherichia coli Proteins - metabolism Life Sciences Membrane Biology Models, Molecular Multiprotein Complexes Nucleotides Protease Protein Conformation Protein folding Protein Structure Protein Unfolding Proteinase Proteins Proteolysis Substrates Trans-Activators - metabolism Translocation
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Summary:	The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis. A spiral of pore loop–substrate contacts spans both ClpA AAA+ domains. Protomers at the spiral seam undergo nucleotide-specific rearrangements, supporting substrate translocation. IGL loops extend flexibly to bind the planar, heptameric ClpP surface with the empty, symmetry-mismatched IGL pocket maintained at the seam. Three different structures identify a binding-pocket switch by the IGL loop of the lowest positioned protomer, involving release and re-engagement with the clockwise pocket. This switch is coupled to a ClpA rotation and a network of conformational changes across the seam, suggesting that ClpA can rotate around the ClpP apical surface during processive steps of translocation and proteolysis. Cryo-EM structures of Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis reveal contacts that drive substrate translocation and a dynamic switch mechanism at the ClpA–ClpP interface.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-3 content type line 23 ObjectType-Undefined-2 These authors contributed equally to this work Author Contributions K.E.L. and A.N.R. carried out all experiments, refinement, and modeling procedures for structure determination, developed figures and wrote and edited the manuscript. E.T. operated Krios microscope and helped with data collection. J.B.L. performed biochemical substrate binding experiments. N.W.S expressed and purified protein components; A.C.T. performed degradation assays; A.L.L. and J.S. wrote and edited the manuscript; D.R.S. designed and supervised the project and wrote and edited the manuscript.
ISSN:	1545-9993 1545-9985
DOI:	10.1038/s41594-020-0409-5