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Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.

ABSTRACT: 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 ?-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic ?-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 ?-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes.

SUBMITTER: Desguin B

PROVIDER: S-EPMC7583248 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.

Desguin Benoît B Urdiain-Arraiza Julian J Da Costa Matthieu M Fellner Matthias M Hu Jian J Hausinger Robert P RP Desmet Tom T Hols Pascal P Soumillion Patrice P

Scientific reports 20201022 1

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 mala ...[more]

PMID: 33093595

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Dataset Information

Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.

Publications

Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.

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