Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism

Proteins
Liang ShiDong-Cai Liang

Abstract

Glycerophosphodiester phosphodiesterase (GDPD; EC 3.1.4.46) catalyzes the hydrolysis of a glycerophosphodiester to an alcohol and glycerol 3-phosphate in glycerol metabolism. It has an important role in the synthesis of a variety of products that participate in many biochemical pathways. We report the crystal structure of the Thermoanaerobacter tengcongensis GDPD (ttGDPD) at 1.91 A resolution, with a calcium ion and glycerol as a substrate mimic coordinated at this calcium ion (PDB entry 2pz0). The ttGDPD dimer with an intermolecular disulfide bridge and two hydrogen bonds is considered as the potential functional unit. We used site-directed mutagenesis to characterize ttGDPD as a metal ion-dependent enzyme, identified a cluster of residues involved in substrate binding and the catalytic reaction, and we propose a possible general acid-base catalytic mechanism for ttGDPD. Superposing the active site with the homologous structure GDPD from Agrobacterium tumefaciens (PDB entry 1zcc), which binds a sulfate ion in the active site, the sulfate ion can represent the phosphate moiety of the substrate, simulating the binding mode of the true substrate of GDPD.

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Citations

Apr 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Supachai TopanurakMaurice B Burg
Jan 19, 2013·Science·Sungjin ParkShanthini Sockanathan
Oct 21, 2015·Toxicon : Official Journal of the International Society on Toxinology·Daniel M Lajoie, Matthew H J Cordes
Jan 1, 2014·The FEBS Journal·Daniela CordaStefania Mariggiò
May 28, 2011·Biochemical and Biophysical Research Communications·Priscila Oliveira de GiuseppeRaghuvir Krishnaswamy Arni
Apr 18, 2012·FEMS Microbiology Letters·Jonathan D Kornspan, Shlomo Rottem
Jun 9, 2016·The Journal of Biological Chemistry·Anneleen CornelissenDouwe van Sinderen
Mar 11, 2015·The Journal of Biological Chemistry·Daniel M LajoieMatthew H J Cordes
Dec 20, 2018·BMC Evolutionary Biology·Matthew H J Cordes, Greta J Binford
Feb 19, 2021·FEBS Open Bio·Takayuki OyamaDaisuke Sugimori

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