Structure of 4-pyridoxolactonase from Mesorhizobium loti.
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.
Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
Jun
J
Kobayashi
Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
Yu
Y
Yoshikane
Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
Toshiharu
T
Yagi
Japan Synchrotron Radiation Research Institute (SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.
Seiki
S
Baba
Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
Kimihiko
K
Mizutani
Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
Nobuyuki
N
Takahashi
Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
Bunzo
B
Mikami
D001665:Binding Sites; D001667:Binding, Competitive; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000378:metabolism*; D020134:Catalytic Domain; D003460:Crystallization; D018360:Crystallography, X-Ray; D059128:Mesorhizobium / Q000201:enzymology*; D008958:Models, Molecular; D011487:Protein Conformation; D011730:Pyridoxal / Q000031:analogs & derivatives* / Q000378:metabolism; D011735:Pyridoxic Acid / Q000378:metabolism*; D015032:Zinc / Q000378:metabolism
C539642:4-pyridoxolactone; D011730:Pyridoxal; D011735:Pyridoxic Acid; C050712:4-pyridoxolactonase; D002265:Carboxylic Ester Hydrolases; D015032:Zinc
4-pyridoxolactonase; Mesorhizobium loti; catalytic mechanisms; docking simulation; vitamin B6; zinc-dependent hydrolase