The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family

Sci Rep. 2018 Jan 16;8(1):865. doi: 10.1038/s41598-018-19192-6.


The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind different types of [Fe-S] clusters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Biocatalysis
  • Catalytic Domain
  • Caulobacter crescentus / enzymology
  • Crystallography, X-Ray
  • Hydro-Lyases / chemistry*
  • Hydro-Lyases / metabolism
  • Magnesium / chemistry
  • Magnesium / metabolism
  • Protein Structure, Quaternary
  • Sequence Alignment
  • Substrate Specificity


  • D-xylo-aldonate dehydratase
  • Hydro-Lyases
  • Magnesium