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

Abstract

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 Dxylopyranose 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 Fe 2+ . 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 Fe 2+ . 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 Ca 2+ , Mg 2+ , or Zn 2+ 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 Fe 2+ as a catalytic metal. This could further expand our understanding of utilization of Fe 2+ not only in oxidative enzymes but also in hydrolases.

Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways

“…However, two genes encoding putative lactonases have been identified elsewhere in the S. solfataricus genome, but the involvement of these genes in pentose degradation is not yet clear. Structural information of pentonolactones is very limited and only very recently have crystal structures of xylonolactonase from C. crescentus complexed with d -xylose and 4-hydroxy-2-pyrrolidinone become available (PDB codes 7PLB, 7PLC and 7PLD) [ 48 ]. This enzyme, which is found in C. crescentus in the same operon as in the genes for the Cc XylB dehydrogenase and Cc XylD dehydratase enzymes, has been shown to improve formation of d -xylonic acid in in vitro enzyme cascade studies [ 49 ].…”

“…Although the SMP30 proteins have a lid-like structure that partly covers the substrate entrance [ 51 ], no such lid exists in C. crescentus xylonolactonase [ 46 ] or X. campestris gluconolactonase [ 49 ]. The crystal structures of C. crescentus xylonolactonase complexed with d -xylose or the substrate analogue 4-hydroxy-2-pyrrolidinone reveal the binding mode of the substrates [ 48 ]. d -xylose was observed in xylopyranose form and the equatorial O1 was bound to the Fe 2+ ion over a short distance of 2.0 Å.…”

“…. crescentus complexed with d-xylose and 4-hydroxy-2-pyrrolidinone become available (PDB codes 7PLB, 7PLC and 7PLD)[48]. This enzyme, which is found in C. crescentus in the same operon as in the genes for the Cc XylB dehydrogenase and Cc XylD dehydratase enzymes, has been shown to improve formation of d-xylonic acid in in vitro enzyme cascade studies…”