An allosteric model for control of pore opening by substrate binding in the E ut L microcompartment shell protein
Abstract
Abstract The ethanolamine utilization (Eut) microcompartment is a protein‐based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC‐domain shell proteins, which form a semi‐permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X‐ray crystal structures of EutL from Clostridium perfringens , along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed‐pore conformation and which is incompatible with opening of the large poremore »
- Authors:
-
- Department of Chemistry and Biochemistry University of California Los Angeles California 90095
- UCLA‐DOE Institute for Genomics and Proteomics, University of California Los Angeles California 90095
- Department of Chemistry and Biochemistry University of California Los Angeles California 90095, UCLA‐DOE Institute for Genomics and Proteomics, University of California Los Angeles California 90095
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1400910
- Grant/Contract Number:
- DE‐FC02‐02ER63421
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Protein Science
- Additional Journal Information:
- Journal Name: Protein Science Journal Volume: 24 Journal Issue: 6; Journal ID: ISSN 0961-8368
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Thompson, Michael C., Cascio, Duilio, Leibly, David J., and Yeates, Todd O. An allosteric model for control of pore opening by substrate binding in the E ut L microcompartment shell protein. United Kingdom: N. p., 2015.
Web. doi:10.1002/pro.2672.
Thompson, Michael C., Cascio, Duilio, Leibly, David J., & Yeates, Todd O. An allosteric model for control of pore opening by substrate binding in the E ut L microcompartment shell protein. United Kingdom. https://doi.org/10.1002/pro.2672
Thompson, Michael C., Cascio, Duilio, Leibly, David J., and Yeates, Todd O. Tue .
"An allosteric model for control of pore opening by substrate binding in the E ut L microcompartment shell protein". United Kingdom. https://doi.org/10.1002/pro.2672.
@article{osti_1400910,
title = {An allosteric model for control of pore opening by substrate binding in the E ut L microcompartment shell protein},
author = {Thompson, Michael C. and Cascio, Duilio and Leibly, David J. and Yeates, Todd O.},
abstractNote = {Abstract The ethanolamine utilization (Eut) microcompartment is a protein‐based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC‐domain shell proteins, which form a semi‐permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X‐ray crystal structures of EutL from Clostridium perfringens , along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed‐pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism we propose is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function. Furthermore, our results suggest the possibility of redox modulation of the allosteric mechanism, opening potentially new lines of investigation.},
doi = {10.1002/pro.2672},
journal = {Protein Science},
number = 6,
volume = 24,
place = {United Kingdom},
year = {Tue Mar 31 00:00:00 EDT 2015},
month = {Tue Mar 31 00:00:00 EDT 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1002/pro.2672
https://doi.org/10.1002/pro.2672
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 25 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Radical Catalysis in Coenzyme B 12 -Dependent Isomerization (Eliminating) Reactions
journal, June 2003
- Toraya, Tetsuo
- Chemical Reviews, Vol. 103, Issue 6
Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster.
journal, March 1995
- Stojiljkovic, I.; Bäumler, A. J.; Heffron, F.
- Journal of Bacteriology, Vol. 177, Issue 5
Ethanolamine Catabolism by Bacteria, Including Escherichia coli
journal, June 1976
- Blackwell, Carol M.; Scarlett, F. Anne; Turner, John M.
- Biochemical Society Transactions, Vol. 4, Issue 3
Linking Crystallographic Model and Data Quality
journal, May 2012
- Karplus, P. A.; Diederichs, K.
- Science, Vol. 336, Issue 6084
Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions
journal, August 2001
- Juers, Douglas H.; Matthews, Brian W.
- Journal of Molecular Biology, Vol. 311, Issue 4
Electrostatics of nanosystems: Application to microtubules and the ribosome
journal, August 2001
- Baker, N. A.; Sept, D.; Joseph, S.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041
Evidence for the formation of disulfide radicals in protein crystals upon X-ray irradiation
journal, November 2002
- Weik, Martin; Bergès, Jacqueline; Raves, Maria L.
- Journal of Synchrotron Radiation, Vol. 9, Issue 6
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
journal, January 2003
- Glaser, F.; Pupko, T.; Paz, I.
- Bioinformatics, Vol. 19, Issue 1
Trimethylamine N -oxide as a versatile cryoprotective agent in macromolecular crystallography
journal, February 2011
- Mueller-Dieckmann, Christoph; Kauffmann, Brice; Weiss, Manfred S.
- Journal of Applied Crystallography, Vol. 44, Issue 2
Role of intestinal bacteria in nutrient metabolism
journal, February 1997
- Cummings, J. H.; Macfarlane, G. T.
- Clinical Nutrition, Vol. 16, Issue 1
Gut flora in health and disease
journal, February 2003
- Guarner, Francisco; Malagelada, Juan-R
- The Lancet, Vol. 361, Issue 9356
The 17-Gene Ethanolamine (eut) Operon ofSalmonella typhimurium Encodes Five Homologues of Carboxysome Shell Proteins
journal, September 1999
- Kofoid, Eric; Rappleye, Chad; Stojiljkovic, Igor
- Journal of Bacteriology, Vol. 181, Issue 17
A breathtaking feat: to compete with the gut microbiota,
journal, January 2011
- Winter, Sebastian E.; Bäumler, Andreas J.
- Gut Microbes, Vol. 2, Issue 1
Ethanolamine Deaminase, a Cobamide Coenzyme-dependent Enzyme
journal, April 1968
- Kaplan, B. H.; Stadtman, E. R.
- Journal of Biological Chemistry, Vol. 243, Issue 8
The pore dimensions of gramicidin A
journal, December 1993
- Smart, O. S.; Goodfellow, J. M.; Wallace, B. A.
- Biophysical Journal, Vol. 65, Issue 6
Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012
- Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
The phosphoglyceride composition of gram-negative bacteria and the changes in composition during growth
journal, September 1969
- Randle, Charlotte L.; Albro, Phillip W.; Dittmer, John C.
- Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, Vol. 187, Issue 2
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation
journal, September 2009
- Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10
Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment
journal, May 2009
- Sagermann, M.; Ohtaki, A.; Nikolakakis, K.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 22
Structural Symmetry and Protein Function
journal, June 2000
- Goodsell, David S.; Olson, Arthur J.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 29, Issue 1
Modelling dynamics in protein crystal structures by ensemble refinement
journal, December 2012
- Burnley, B. Tom; Afonine, Pavel V.; Adams, Paul D.
- eLife, Vol. 1
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
journal, May 1995
- Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.
- Journal of the American Chemical Society, Vol. 117, Issue 19
Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors
journal, April 2009
- Li, Hua; Kristensen, David M.; Coleman, Michael K.
- PLoS ONE, Vol. 4, Issue 4
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Non-dietary lipid in the intestinal lumen
journal, September 1972
- Cotton, P. B.
- Gut, Vol. 13, Issue 9
Global regulation by CsrA in Salmonella typhimurium: S. typhimurium CsrA global regulation
journal, May 2003
- Lawhon, Sara D.; Frye, Jonathan G.; Suyemoto, Mitsu
- Molecular Microbiology, Vol. 48, Issue 6
Consumption of Fermented Milk Product With Probiotic Modulates Brain Activity
journal, June 2013
- Tillisch, Kirsten; Labus, Jennifer; Kilpatrick, Lisa
- Gastroenterology, Vol. 144, Issue 7
Specific chemical and structural damage to proteins produced by synchrotron radiation
journal, January 2000
- Weik, M.; Ravelli, R. B. G.; Kryger, G.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 2
Conserving a Volatile Metabolite: a Role for Carboxysome-Like Organelles in Salmonella enterica
journal, April 2006
- Penrod, J. T.; Roth, J. R.
- Journal of Bacteriology, Vol. 188, Issue 8
Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota
journal, October 2011
- Thiennimitr, P.; Winter, S. E.; Winter, M. G.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 42
Ethanolamine utilization in Salmonella typhimurium.
journal, September 1988
- Roof, D. M.; Roth, J. R.
- Journal of Bacteriology, Vol. 170, Issue 9
Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell
journal, September 2010
- Crowley, Christopher S.; Cascio, Duilio; Sawaya, Michael R.
- Journal of Biological Chemistry, Vol. 285, Issue 48
Ethanolamine utilization in bacterial pathogens: roles and regulation
journal, April 2010
- Garsin, Danielle A.
- Nature Reviews Microbiology, Vol. 8, Issue 4
Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor
journal, November 2014
- Thompson, Michael C.; Crowley, Christopher S.; Kopstein, Jeffrey
- Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 12
Radiation damage in macromolecular crystallography: what is it and why should we care?
journal, March 2010
- Garman, Elspeth F.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Evidence that a Metabolic Microcompartment Contains and Recycles Private Cofactor Pools
journal, April 2013
- Huseby, D. L.; Roth, J. R.
- Journal of Bacteriology, Vol. 195, Issue 12
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Allergy development and the intestinal microflora during the first year of life
journal, October 2001
- Björkstén, Bengt; Sepp, Epp; Julge, Kaja
- Journal of Allergy and Clinical Immunology, Vol. 108, Issue 4
Crystallographic Insights into the Pore Structures and Mechanisms of the EutL and EutM Shell Proteins of the Ethanolamine-Utilizing Microcompartment of Escherichia coli
journal, September 2010
- Takenoya, M.; Nikolakakis, K.; Sagermann, M.
- Journal of Bacteriology, Vol. 192, Issue 22
Comparative Genomics of Ethanolamine Utilization
journal, September 2009
- Tsoy, O.; Ravcheev, D.; Mushegian, A.
- Journal of Bacteriology, Vol. 191, Issue 23
Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli
journal, December 2009
- Tanaka, S.; Sawaya, M. R.; Yeates, T. O.
- Science, Vol. 327, Issue 5961
Who controls the crowd? New findings and old questions about the intestinal microflora
journal, June 2005
- Steinhoff, U.
- Immunology Letters, Vol. 99, Issue 1
Symmetry, stability, and dynamics of multidomain and multicomponent protein systems
journal, December 1996
- Blundell, T. L.; Srinivasan, N.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 25
Gut inflammation provides a respiratory electron acceptor for Salmonella
journal, September 2010
- Winter, Sebastian E.; Thiennimitr, Parameth; Winter, Maria G.
- Nature, Vol. 467, Issue 7314
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB
journal, November 2012
- Pang, Allan; Liang, Mingzhi; Prentice, Michael B.
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 12
Structural changes in a cryo-cooled protein crystal owing to radiation damage
journal, March 2000
- Burmeister, Wilhelm Pascal
- Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 3
Analysis and Functional Prediction of Reactive Cysteine Residues
journal, December 2011
- Marino, Stefano M.; Gladyshev, Vadim N.
- Journal of Biological Chemistry, Vol. 287, Issue 7
An obesity-associated gut microbiome with increased capacity for energy harvest
journal, December 2006
- Turnbaugh, Peter J.; Ley, Ruth E.; Mahowald, Michael A.
- Nature, Vol. 444, Issue 7122
Comparison of OG1RF and an Isogenic fsrB Deletion Mutant by Transcriptional Analysis: the Fsr System of Enterococcus faecalis Is More than the Activator of Gelatinase and Serine Protease
journal, April 2006
- Bourgogne, A.; Hilsenbeck, S. G.; Dunny, G. M.
- Journal of Bacteriology, Vol. 188, Issue 8
Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe–4S cluster-binding site
journal, January 2011
- Pang, Allan; Warren, Martin J.; Pickersgill, Richard W.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 2
Systematic Association of Genes to Phenotypes by Genome and Literature Mining
journal, April 2005
- Korbel, Jan O.; Doerks, Tobias; Jensen, Lars J.
- PLoS Biology, Vol. 3, Issue 5
A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium
journal, July 2004
- Kelly, A.
- Microbiology, Vol. 150, Issue 7
Microbial Ecology of the Gastrointestinal Tract
journal, October 1977
- Savage, D. C.
- Annual Review of Microbiology, Vol. 31, Issue 1
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
journal, May 2010
- Ashkenazy, H.; Erez, E.; Martz, E.
- Nucleic Acids Research, Vol. 38, Issue Web Server
The PduQ Enzyme Is an Alcohol Dehydrogenase Used to Recycle NAD+ Internally within the Pdu Microcompartment of Salmonella enterica
journal, October 2012
- Cheng, Shouqiang; Fan, Chenguang; Sinha, Sharmistha
- PLoS ONE, Vol. 7, Issue 10
DNA polymerase I function is required for the utilization of ethanolamine, 1,2-propanediol, and propionate by Salmonella typhimurium LT2.
journal, December 1995
- Rondon, M. R.; Horswill, A. R.; Escalante-Semerena, J. C.
- Journal of Bacteriology, Vol. 177, Issue 24
Identification of a Reactivating Factor for Adenosylcobalamin-Dependent Ethanolamine Ammonia Lyase
journal, October 2004
- Mori, K.; Bando, R.; Hieda, N.
- Journal of Bacteriology, Vol. 186, Issue 20
The eutT Gene of Salmonella enterica Encodes an Oxygen-Labile, Metal-Containing ATP:Corrinoid Adenosyltransferase Enzyme
journal, August 2004
- Buan, N. R.; Suh, S. -J.; Escalante-Semerena, J. C.
- Journal of Bacteriology, Vol. 186, Issue 17
A dynamic partnership: Celebrating our gut flora
journal, October 2005
- Sears, Cynthia L.
- Anaerobe, Vol. 11, Issue 5
Multi-template approach to modeling engineered disulfide bonds
journal, June 2006
- Pellequer, Jean-Luc; Chen, Shu-wen W.
- Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 1
Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport
journal, September 2009
- Klein, Michael G.; Zwart, Peter; Bagby, Sarah C.
- Journal of Molecular Biology, Vol. 392, Issue 2
Accessing protein conformational ensembles using room-temperature X-ray crystallography
journal, September 2011
- Fraser, J. S.; van den Bedem, H.; Samelson, A. J.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 39
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Tetrathionate reduction and production of hydrogen sulfide from thiosulfate.
journal, January 1987
- Barrett, E. L.; Clark, M. A.
- Microbiological Reviews, Vol. 51, Issue 2
Human gut microbes associated with obesity
journal, December 2006
- Ley, Ruth E.; Turnbaugh, Peter J.; Klein, Samuel
- Nature, Vol. 444, Issue 7122
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Crystallographic fast Fourier transforms
journal, March 1973
- Ten Eyck, L. F.
- Acta Crystallographica Section A, Vol. 29, Issue 2
Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri
journal, September 2009
- Heldt, Dana; Frank, Stefanie; Seyedarabi, Arefeh
- Biochemical Journal, Vol. 423, Issue 2