Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.

Karen McLuskey; Jaspreet Grewal; Debanu Das; Adam Godzik; Scott A. Lesley; Ashley M. Deacon; Graham H. Coombs; Marc-Andre Elslinger; Ian A. Wilson; Jeremy Charles Mottram

doi:10.1074/jbc.M115.706143

Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.

Karen McLuskey, Jaspreet Grewal, Debanu Das, Adam Godzik, Scott A. Lesley, Ashley M. Deacon, Graham H. Coombs, Marc-Andre Elslinger, Ian A. Wilson, Jeremy Charles Mottram

Biology

Research output: Contribution to journal › Article › peer-review

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 K147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed K147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an auto-inhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts both Arg and Lys substrates and does not require Ca2+ for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.

Original language	English
Pages (from-to)	9482-9491
Number of pages	10
Journal	Journal of Biological Chemistry
Volume	291
Issue number	18
Early online date	3 Mar 2016
DOIs	https://doi.org/10.1074/jbc.M115.706143
Publication status	E-pub ahead of print - 3 Mar 2016

Bibliographical note

Copyright 2016 by The American Society for Biochemistry and Molecular Biology, Inc. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.

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10.1074/jbc.M115.706143

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Copyright 2016 by The American Society for Biochemistry and Molecular Biology, Inc. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.
Accepted author manuscript, 1.48 MBLicence: CC BY

Cite this

McLuskey, K., Grewal, J., Das, D., Godzik, A., Lesley, S. A., Deacon, A. M., Coombs, G. H., Elslinger, M.-A., Wilson, I. A., & Mottram, J. C. (2016). Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome. Journal of Biological Chemistry, 291(18), 9482-9491. Advance online publication. https://doi.org/10.1074/jbc.M115.706143

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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 {\AA} 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 K147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed K147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an auto-inhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts both Arg and Lys substrates and does not require Ca2+ for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.",

author = "Karen McLuskey and Jaspreet Grewal and Debanu Das and Adam Godzik and Lesley, {Scott A.} and Deacon, {Ashley M.} and Coombs, {Graham H.} and Marc-Andre Elslinger and Wilson, {Ian A.} and Mottram, {Jeremy Charles}",

note = "Copyright 2016 by The American Society for Biochemistry and Molecular Biology, Inc. This is an author-produced version of the published paper. Uploaded in accordance with the publisher{\textquoteright}s self-archiving policy. Further copying may not be permitted; contact the publisher for details.",

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AU - Godzik, Adam

AU - Lesley, Scott A.

AU - Deacon, Ashley M.

AU - Coombs, Graham H.

AU - Elslinger, Marc-Andre

AU - Wilson, Ian A.

AU - Mottram, Jeremy Charles

N1 - Copyright 2016 by The American Society for Biochemistry and Molecular Biology, Inc. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.

PY - 2016/3/3

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N2 - 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 K147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed K147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an auto-inhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts both Arg and Lys substrates and does not require Ca2+ for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.

AB - 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 K147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed K147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an auto-inhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts both Arg and Lys substrates and does not require Ca2+ for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.

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