Three-dimensional structure of xylonolactonase from Caulobacter crescentus: A mononuclear iron enzyme of the 6-bladed β-propeller hydrolase family

Protein Sci. 2022 Feb;31(2):371-383. doi: 10.1002/pro.4229. Epub 2021 Nov 20.


Xylonolactonase Cc XylC from Caulobacter crescentus catalyzes the hydrolysis of the intramolecular ester bond of d-xylonolactone. We have determined crystal structures of Cc XylC in complex with d-xylonolactone isomer analogues d-xylopyranose and (r)-(+)-4-hydroxy-2-pyrrolidinone at high resolution. Cc XylC has a 6-bladed β-propeller architecture, which contains a central open channel having the active site at one end. According to our previous native mass spectrometry studies, Cc XylC is able to specifically bind Fe2+ . The crystal structures, presented here, revealed an active site bound metal ion with an octahedral binding geometry. The side chains of three amino acid residues, Glu18, Asn146, and Asp196, which participate in binding of metal ion are located in the same plane. The solved complex structures allowed suggesting a reaction mechanism for intramolecular ester bond hydrolysis in which the major contribution for catalysis arises from the carbonyl oxygen coordination of the xylonolactone substrate to the Fe2+ . The structure of Cc XylC was compared with eight other ester hydrolases of the β-propeller hydrolase family. The previously published crystal structures of other β-propeller hydrolases contain either Ca2+ , Mg2+ , or Zn2+ and show clear similarities in ligand and metal ion binding geometries to that of Cc XylC. It would be interesting to reinvestigate the metal binding specificity of these enzymes and clarify whether they are also able to use Fe2+ as a catalytic metal. This could further expand our understanding of utilization of Fe2+ not only in oxidative enzymes but also in hydrolases.

Keywords: Caulobacter crescentus; crystal structure; enzyme mechanism; hydrolase; iron; metal coordination; metalloenzyme; xylonolactonase; β-propeller hydrolase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carboxylic Ester Hydrolases* / chemistry
  • Carboxylic Ester Hydrolases* / metabolism
  • Catalytic Domain
  • Caulobacter crescentus* / enzymology
  • Crystallography, X-Ray
  • Hydrolases
  • Hydrolysis
  • Iron
  • Lactones / chemistry
  • Lactones / metabolism


  • Lactones
  • Iron
  • Hydrolases
  • Carboxylic Ester Hydrolases