Structural and Functional Diversity of the Microbial Kinome

The eukaryotic protein kinase (ePK) domain mediates the majority of signaling and coordination of complex events in eukaryotes. By contrast, most bacterial signaling is thought to occur through structurally unrelated histidine kinases, though some ePK-like kinases (ELKs) and small molecule kinases a...

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Autores principales: Kannan, Natarajan, Taylor, Susan S, Zhai, Yufeng, Venter, J. Craig, Manning, Gerard
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821047/
https://www.ncbi.nlm.nih.gov/pubmed/17355172
http://dx.doi.org/10.1371/journal.pbio.0050017
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author Kannan, Natarajan
Taylor, Susan S
Zhai, Yufeng
Venter, J. Craig
Manning, Gerard
author_facet Kannan, Natarajan
Taylor, Susan S
Zhai, Yufeng
Venter, J. Craig
Manning, Gerard
author_sort Kannan, Natarajan
collection PubMed
description The eukaryotic protein kinase (ePK) domain mediates the majority of signaling and coordination of complex events in eukaryotes. By contrast, most bacterial signaling is thought to occur through structurally unrelated histidine kinases, though some ePK-like kinases (ELKs) and small molecule kinases are known in bacteria. Our analysis of the Global Ocean Sampling (GOS) dataset reveals that ELKs are as prevalent as histidine kinases and may play an equally important role in prokaryotic behavior. By combining GOS and public databases, we show that the ePK is just one subset of a diverse superfamily of enzymes built on a common protein kinase–like (PKL) fold. We explored this huge phylogenetic and functional space to cast light on the ancient evolution of this superfamily, its mechanistic core, and the structural basis for its observed diversity. We cataloged 27,677 ePKs and 18,699 ELKs, and classified them into 20 highly distinct families whose known members suggest regulatory functions. GOS data more than tripled the count of ELK sequences and enabled the discovery of novel families and classification and analysis of all ELKs. Comparison between and within families revealed ten key residues that are highly conserved across families. However, all but one of the ten residues has been eliminated in one family or another, indicating great functional plasticity. We show that loss of a catalytic lysine in two families is compensated by distinct mechanisms both involving other key motifs. This diverse superfamily serves as a model for further structural and functional analysis of enzyme evolution.
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spelling pubmed-18210472007-03-14 Structural and Functional Diversity of the Microbial Kinome Kannan, Natarajan Taylor, Susan S Zhai, Yufeng Venter, J. Craig Manning, Gerard PLoS Biol Research Article The eukaryotic protein kinase (ePK) domain mediates the majority of signaling and coordination of complex events in eukaryotes. By contrast, most bacterial signaling is thought to occur through structurally unrelated histidine kinases, though some ePK-like kinases (ELKs) and small molecule kinases are known in bacteria. Our analysis of the Global Ocean Sampling (GOS) dataset reveals that ELKs are as prevalent as histidine kinases and may play an equally important role in prokaryotic behavior. By combining GOS and public databases, we show that the ePK is just one subset of a diverse superfamily of enzymes built on a common protein kinase–like (PKL) fold. We explored this huge phylogenetic and functional space to cast light on the ancient evolution of this superfamily, its mechanistic core, and the structural basis for its observed diversity. We cataloged 27,677 ePKs and 18,699 ELKs, and classified them into 20 highly distinct families whose known members suggest regulatory functions. GOS data more than tripled the count of ELK sequences and enabled the discovery of novel families and classification and analysis of all ELKs. Comparison between and within families revealed ten key residues that are highly conserved across families. However, all but one of the ten residues has been eliminated in one family or another, indicating great functional plasticity. We show that loss of a catalytic lysine in two families is compensated by distinct mechanisms both involving other key motifs. This diverse superfamily serves as a model for further structural and functional analysis of enzyme evolution. Public Library of Science 2007-03 2007-03-13 /pmc/articles/PMC1821047/ /pubmed/17355172 http://dx.doi.org/10.1371/journal.pbio.0050017 Text en © 2007 Kannan et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Kannan, Natarajan
Taylor, Susan S
Zhai, Yufeng
Venter, J. Craig
Manning, Gerard
Structural and Functional Diversity of the Microbial Kinome
title Structural and Functional Diversity of the Microbial Kinome
title_full Structural and Functional Diversity of the Microbial Kinome
title_fullStr Structural and Functional Diversity of the Microbial Kinome
title_full_unstemmed Structural and Functional Diversity of the Microbial Kinome
title_short Structural and Functional Diversity of the Microbial Kinome
title_sort structural and functional diversity of the microbial kinome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821047/
https://www.ncbi.nlm.nih.gov/pubmed/17355172
http://dx.doi.org/10.1371/journal.pbio.0050017
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