ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores

Mark F Mabanglo; Elisa Leung; Siavash Vahidi; Thiago V Seraphim; Bryan T Eger; Steve Bryson; Vaibhav Bhandari; Jin Lin Zhou; Yu-Qian Mao; Kamran Rizzolo; Marim M Barghash; Jordan D Goodreid; Sadhna Phanse; Mohan Babu; Leandro R S Barbosa; Carlos H I Ramos; Robert A Batey; Lewis E Kay; Emil F Pai; Walid A Houry

doi:10.1038/s42003-019-0656-3

ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores

Commun Biol. 2019 Nov 13:2:410. doi: 10.1038/s42003-019-0656-3. eCollection 2019.

Authors

Mark F Mabanglo^#¹, Elisa Leung^#¹, Siavash Vahidi^#^{1

2

3

4}, Thiago V Seraphim^#^{1

5}, Bryan T Eger¹, Steve Bryson^{1

6}, Vaibhav Bhandari¹, Jin Lin Zhou³, Yu-Qian Mao¹, Kamran Rizzolo¹, Marim M Barghash¹, Jordan D Goodreid³, Sadhna Phanse^{1

5}, Mohan Babu⁵, Leandro R S Barbosa⁷, Carlos H I Ramos⁸, Robert A Batey³, Lewis E Kay^{1

2

3

4}, Emil F Pai^{1

2

6

9}, Walid A Houry^{1

3}

Affiliations

¹ 1Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada.
² 2Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada.
³ 3Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada.
⁴ 4Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada.
⁵ 5Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada.
⁶ 6Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada.
⁷ 7Institute of Physics, University of São Paulo, São Paulo SP, 05508-090 Brazil.
⁸ 8Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil.
⁹ 9Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8 Canada.

^# Contributed equally.

Abstract

Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.

Keywords: Proteases; X-ray crystallography.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Binding Sites
Crystallography, X-Ray
Endopeptidase Clp / chemistry*
Endopeptidase Clp / metabolism
Enzyme Activation
Magnetic Resonance Spectroscopy
Models, Molecular*
Molecular Docking Simulation
Molecular Dynamics Simulation
Protein Binding
Protein Tyrosine Phosphatases / chemistry
Static Electricity*

Substances

Protein Tyrosine Phosphatases
Endopeptidase Clp

Abstract

Publication types

MeSH terms

Substances

Grants and funding