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

Nat Commun. 2021 Nov 18;12(1):6717. doi: 10.1038/s41467-021-27105-x.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Asparaginase / chemistry
  • Asparaginase / genetics
  • Asparaginase / metabolism*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Binding Sites / genetics
  • Biocatalysis
  • Catalytic Domain*
  • Cations / chemistry
  • Cations / metabolism
  • Crystallography, X-Ray
  • Enzyme Stability
  • Hydrogen-Ion Concentration
  • Kinetics
  • Metals / chemistry
  • Metals / metabolism
  • Models, Molecular
  • Mutation
  • Protein Binding
  • Protein Folding
  • Protein Multimerization
  • Rhizobium etli / enzymology*
  • Rhizobium etli / genetics
  • Temperature

Substances

  • Bacterial Proteins
  • Cations
  • Metals
  • Asparaginase