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Title: Crystal structure and activity studies of the C11 cysteine peptidase from Parabacteroides merdae in the human gut microbiome

Abstract

Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms. However, for the clostripain family (denoted C11), little is currently known. Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution. PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain. It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other families in the clan. These studies also revealed a well ordered break in the polypeptide chain at Lys147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity. Altogether, these data provide insights into the mechanism and activity of PmC11 and a detailedmore » framework for studies on C11 peptidases from other phylogenetic kingdoms.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [4];  [5];  [3];  [6];  [7];  [7]; ORCiD logo [2]
  1. Univ. of Glasgow, Glasgow (United Kingdom)
  2. Univ. of Glasgow, Glasgow (United Kingdom); Univ. of York, York (United Kingdom)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  4. SLAC National Accelerator Lab., Menlo Park, CA (United States); Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA (United States)
  5. SLAC National Accelerator Lab., Menlo Park, CA (United States); The Scripps Research Institute, La Jolla, CA (United States); Genomics Institute of the Novartis Research Foundation, San Diego, CA (United States)
  6. Univ. of Strathclyde, Glasgow (United Kingdom)
  7. SLAC National Accelerator Lab., Menlo Park, CA (United States); The Scripps Research Institute, La Jolla, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1256314
Grant/Contract Number:  
MR/K019384; 091790; 104111; GM094586; AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 291; Journal Issue: 18; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; C-terminal domain (carboxyl tail domain, CTD); crystal structure; cysteine protease; enzyme; proteolysis; active site; domain; kinteoplast

Citation Formats

McLuskey, Karen, Grewal, Jaspreet S., Das, Debanu, Godzik, Adam, Lesley, Scott A., Deacon, Ashley M., Coombs, Graham H., Elsliger, Marc-André, Wilson, Ian A., and Mottram, Jeremy C.. Crystal structure and activity studies of the C11 cysteine peptidase from Parabacteroides merdae in the human gut microbiome. United States: N. p., 2016. Web. https://doi.org/10.1074/jbc.M115.706143.
McLuskey, Karen, Grewal, Jaspreet S., Das, Debanu, Godzik, Adam, Lesley, Scott A., Deacon, Ashley M., Coombs, Graham H., Elsliger, Marc-André, Wilson, Ian A., & Mottram, Jeremy C.. Crystal structure and activity studies of the C11 cysteine peptidase from Parabacteroides merdae in the human gut microbiome. United States. https://doi.org/10.1074/jbc.M115.706143
McLuskey, Karen, Grewal, Jaspreet S., Das, Debanu, Godzik, Adam, Lesley, Scott A., Deacon, Ashley M., Coombs, Graham H., Elsliger, Marc-André, Wilson, Ian A., and Mottram, Jeremy C.. Thu . "Crystal structure and activity studies of the C11 cysteine peptidase from Parabacteroides merdae in the human gut microbiome". United States. https://doi.org/10.1074/jbc.M115.706143. https://www.osti.gov/servlets/purl/1256314.
@article{osti_1256314,
title = {Crystal structure and activity studies of the C11 cysteine peptidase from Parabacteroides merdae in the human gut microbiome},
author = {McLuskey, Karen and Grewal, Jaspreet S. and Das, Debanu and Godzik, Adam and Lesley, Scott A. and Deacon, Ashley M. and Coombs, Graham H. and Elsliger, Marc-André and Wilson, Ian A. and Mottram, Jeremy C.},
abstractNote = {Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms. However, for the clostripain family (denoted C11), little is currently known. Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution. PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain. It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other families in the clan. These studies also revealed a well ordered break in the polypeptide chain at Lys147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity. Altogether, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.},
doi = {10.1074/jbc.M115.706143},
journal = {Journal of Biological Chemistry},
number = 18,
volume = 291,
place = {United States},
year = {2016},
month = {3}
}

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