Structure of 4-pyridoxolactonase from Mesorhizobium loti

  • Acta Crystallogr F Struct Biol Commun. 2014 Apr;70(Pt 4):424-32. doi: 10.1107/S2053230X14003926.
Jun Kobayashi  1 ,  Yu Yoshikane  2 ,  Toshiharu Yagi  2 ,  Seiki Baba  3 ,  Kimihiko Mizutani  1 ,  Nobuyuki Takahashi  1 ,  Bunzo Mikami  1
Affiliations
  • 1. Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
  • 2. Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
  • 3. Japan Synchrotron Radiation Research Institute (SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.
PMID: 24699732 DOI: 10.1107/S2053230X14003926
Abstract

4-Pyridoxolactonase from Mesorhizobium loti catalyzes the zinc-dependent lactone-ring hydrolysis of 4-pyridoxolactone (4PAL) to 4-pyridoxic acid (4PA) in vitamin B6 degradation pathway I. The crystal structures of 4-pyridoxolactonase and its complex with 5-pyridoxolactone (5PAL; the competitive inhibitor) were determined. The overall structure was an αβ/βα sandwich fold, and two zinc ions were coordinated. This strongly suggested that the enzyme belongs to subclass B3 of the class B β-lactamases. In the complex structure, the carbonyl group of 5PAL pointed away from the active site, revealing why it acts as a competitive inhibitor. Based on docking simulation with 4PAL, 4PA and a reaction intermediate, 4-pyridoxolactonase probably catalyzes the reaction through a subclass B2-like mechanism, not the subclass B3 mechanism.

Keywords
4-pyridoxolactonase; Mesorhizobium loti; catalytic mechanisms; docking simulation; vitamin B6; zinc-dependent hydrolase.
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