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Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases

Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes....

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Autores principales: Desguin, Benoît, Urdiain-Arraiza, Julian, Da Costa, Matthieu, Fellner, Matthias, Hu, Jian, Hausinger, Robert P., Desmet, Tom, Hols, Pascal, Soumillion, Patrice
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583248/
https://www.ncbi.nlm.nih.gov/pubmed/33093595
http://dx.doi.org/10.1038/s41598-020-74802-6
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author Desguin, Benoît
Urdiain-Arraiza, Julian
Da Costa, Matthieu
Fellner, Matthias
Hu, Jian
Hausinger, Robert P.
Desmet, Tom
Hols, Pascal
Soumillion, Patrice
author_facet Desguin, Benoît
Urdiain-Arraiza, Julian
Da Costa, Matthieu
Fellner, Matthias
Hu, Jian
Hausinger, Robert P.
Desmet, Tom
Hols, Pascal
Soumillion, Patrice
author_sort Desguin, Benoît
collection PubMed
description Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic α-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes.
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spelling pubmed-75832482020-10-27 Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases Desguin, Benoît Urdiain-Arraiza, Julian Da Costa, Matthieu Fellner, Matthias Hu, Jian Hausinger, Robert P. Desmet, Tom Hols, Pascal Soumillion, Patrice Sci Rep Article Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic α-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes. Nature Publishing Group UK 2020-10-22 /pmc/articles/PMC7583248/ /pubmed/33093595 http://dx.doi.org/10.1038/s41598-020-74802-6 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Desguin, Benoît
Urdiain-Arraiza, Julian
Da Costa, Matthieu
Fellner, Matthias
Hu, Jian
Hausinger, Robert P.
Desmet, Tom
Hols, Pascal
Soumillion, Patrice
Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
title Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
title_full Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
title_fullStr Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
title_full_unstemmed Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
title_short Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
title_sort uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583248/
https://www.ncbi.nlm.nih.gov/pubmed/33093595
http://dx.doi.org/10.1038/s41598-020-74802-6
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