4KEQ

Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound

Summary for 4KEQ

• Entry DOI: 10.2210/pdb4keq/pdb
• Related: 3AJ3 4KEP
• Descriptor: 4-pyridoxolactonase, ZINC ION, 7-hydroxy-6-methylfuro[3,4-c]pyridin-3(1H)-one, ... (6 entities in total)
• Functional Keywords: alpha-beta/beta-alpha fold, hydrolase, lactone
• Biological source: Mesorhizobium loti
• Total number of polymer chains: 1
• Total formula weight: 31649.23

Authors

Kobayashi, J.,Yoshikane, Y.,Baba, S.,Mizutani, K.,Takahashi, N.,Mikami, B.,Yagi, T. (deposition date: 2013-04-26, release date: 2014-04-09, Last modification date: 2023-11-08)

Primary citation

Kobayashi, J.,Yoshikane, Y.,Yagi, T.,Baba, S.,Mizutani, K.,Takahashi, N.,Mikami, B.
Structure of 4-pyridoxolactonase from Mesorhizobium loti.
Acta Crystallogr.,Sect.F, 70:424-432, 2014

PubMed 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.

PubMed: 24699732
DOI: 10.1107/S2053230X14003926

Experimental method

X-RAY DIFFRACTION (2.279 Å)