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RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry

[Image: see text] The radical SAM superfamily (RSS), arguably the most functionally diverse enzyme superfamily, is also one of the largest with ∼700 K members currently in the UniProt database. The vast majority of the members have uncharacterized enzymatic activities and metabolic functions. In thi...

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Autores principales: Oberg, Nils, Precord, Timothy W., Mitchell, Douglas A., Gerlt, John A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2021
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477430/
https://www.ncbi.nlm.nih.gov/pubmed/36119373
http://dx.doi.org/10.1021/acsbiomedchemau.1c00048
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author Oberg, Nils
Precord, Timothy W.
Mitchell, Douglas A.
Gerlt, John A.
author_facet Oberg, Nils
Precord, Timothy W.
Mitchell, Douglas A.
Gerlt, John A.
author_sort Oberg, Nils
collection PubMed
description [Image: see text] The radical SAM superfamily (RSS), arguably the most functionally diverse enzyme superfamily, is also one of the largest with ∼700 K members currently in the UniProt database. The vast majority of the members have uncharacterized enzymatic activities and metabolic functions. In this Perspective, we describe RadicalSAM.org, a new web-based resource that enables a user-friendly genomic enzymology strategy to explore sequence-function space in the RSS. The resource attempts to enable identification of isofunctional groups of radical SAM enzymes using sequence similarity networks (SSNs) and the genome context of the bacterial, archaeal, and fungal members provided by genome neighborhood diagrams (GNDs). Enzymatic activities and in vivo functions frequently can be inferred from genome context given the tendency for genes of related function to be clustered. We invite the scientific community to use RadicalSAM.org to (i) guide their experimental studies to discover new enzymatic activities and metabolic functions, (ii) contribute experimentally verified annotations to RadicalSAM.org to enhance the ability to predict novel activities and functions, and (iii) provide suggestions for improving this resource.
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spelling pubmed-94774302023-02-16 RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry Oberg, Nils Precord, Timothy W. Mitchell, Douglas A. Gerlt, John A. ACS Bio Med Chem Au [Image: see text] The radical SAM superfamily (RSS), arguably the most functionally diverse enzyme superfamily, is also one of the largest with ∼700 K members currently in the UniProt database. The vast majority of the members have uncharacterized enzymatic activities and metabolic functions. In this Perspective, we describe RadicalSAM.org, a new web-based resource that enables a user-friendly genomic enzymology strategy to explore sequence-function space in the RSS. The resource attempts to enable identification of isofunctional groups of radical SAM enzymes using sequence similarity networks (SSNs) and the genome context of the bacterial, archaeal, and fungal members provided by genome neighborhood diagrams (GNDs). Enzymatic activities and in vivo functions frequently can be inferred from genome context given the tendency for genes of related function to be clustered. We invite the scientific community to use RadicalSAM.org to (i) guide their experimental studies to discover new enzymatic activities and metabolic functions, (ii) contribute experimentally verified annotations to RadicalSAM.org to enhance the ability to predict novel activities and functions, and (iii) provide suggestions for improving this resource. American Chemical Society 2021-12-17 /pmc/articles/PMC9477430/ /pubmed/36119373 http://dx.doi.org/10.1021/acsbiomedchemau.1c00048 Text en © 2021 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Oberg, Nils
Precord, Timothy W.
Mitchell, Douglas A.
Gerlt, John A.
RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry
title RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry
title_full RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry
title_fullStr RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry
title_full_unstemmed RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry
title_short RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry
title_sort radicalsam.org: a resource to interpret sequence-function space and discover new radical sam enzyme chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477430/
https://www.ncbi.nlm.nih.gov/pubmed/36119373
http://dx.doi.org/10.1021/acsbiomedchemau.1c00048
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