Crystal structures of the elusive Rhizobium etli l-asparaginase reveal a peculiar active site

Joanna I. Loch, Barbara Imiolczyk, Joanna Sliwiak, Anna Wantuch, Magdalena Bejger, Miroslaw Gilski and Mariusz Jaskolski ()
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Joanna I. Loch: Faculty of Chemistry, Jagiellonian University
Barbara Imiolczyk: Institute of Bioorganic Chemistry, Polish Academy of Sciences
Joanna Sliwiak: Institute of Bioorganic Chemistry, Polish Academy of Sciences
Anna Wantuch: Faculty of Chemistry, Jagiellonian University
Magdalena Bejger: Institute of Bioorganic Chemistry, Polish Academy of Sciences
Miroslaw Gilski: Institute of Bioorganic Chemistry, Polish Academy of Sciences
Mariusz Jaskolski: Institute of Bioorganic Chemistry, Polish Academy of Sciences

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract Rhizobium etli, a nitrogen-fixing bacterial symbiont of legume plants, encodes an essential l-asparaginase (ReAV) with no sequence homology to known enzymes with this activity. High-resolution crystal structures of ReAV show indeed a structurally distinct, dimeric enzyme, with some resemblance to glutaminases and β-lactamases. However, ReAV has no glutaminase or lactamase activity, and at pH 9 its allosteric asparaginase activity is relatively high, with Km for l-Asn at 4.2 mM and kcat of 438 s−1. The active site of ReAV, deduced from structural comparisons and confirmed by mutagenesis experiments, contains a highly specific Zn2+ binding site without a catalytic role. The extensive active site includes residues with unusual chemical properties. There are two Ser-Lys tandems, all connected through a network of H-bonds to the Zn center, and three tightly bound water molecules near Ser48, which clearly indicate the catalytic nucleophile.

Date: 2021
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DOI: 10.1038/s41467-021-27105-x

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