MCPdb: The bacterial microcompartment database.
Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0248269 |
| _version_ | 1818581719178018816 |
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| author | Jessica M Ochoa Kaylie Bair Thomas Holton Thomas A Bobik Todd O Yeates |
| author_facet | Jessica M Ochoa Kaylie Bair Thomas Holton Thomas A Bobik Todd O Yeates |
| author_sort | Jessica M Ochoa |
| collection | DOAJ |
| description | Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, the existing functionalities of current resources have limited our ability to rapidly understand the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphasize the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 163 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria. |
| first_indexed | 2024-12-16T07:37:57Z |
| format | Article |
| id | doaj.art-dc371453c5cd448abb6fedc29ddf9356 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-16T07:37:57Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-dc371453c5cd448abb6fedc29ddf93562022-12-21T22:39:10ZengPublic Library of Science (PLoS)PLoS ONE1932-62032021-01-01163e024826910.1371/journal.pone.0248269MCPdb: The bacterial microcompartment database.Jessica M OchoaKaylie BairThomas HoltonThomas A BobikTodd O YeatesBacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, the existing functionalities of current resources have limited our ability to rapidly understand the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphasize the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 163 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.https://doi.org/10.1371/journal.pone.0248269 |
| spellingShingle | Jessica M Ochoa Kaylie Bair Thomas Holton Thomas A Bobik Todd O Yeates MCPdb: The bacterial microcompartment database. PLoS ONE |
| title | MCPdb: The bacterial microcompartment database. |
| title_full | MCPdb: The bacterial microcompartment database. |
| title_fullStr | MCPdb: The bacterial microcompartment database. |
| title_full_unstemmed | MCPdb: The bacterial microcompartment database. |
| title_short | MCPdb: The bacterial microcompartment database. |
| title_sort | mcpdb the bacterial microcompartment database |
| url | https://doi.org/10.1371/journal.pone.0248269 |
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