Periplasmic glycerophosphodiester phosphodiesterase domain (GlpQ) and similar proteins
This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in bacterial and eukaryotic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ. GP-GDEs are involved in glycerol metabolism and catalyze the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. In E. coli, there are two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the glp operon codes for a periplasmic phosphodiesterase GlpQ. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), to the corresponding alcohols and G3P, which is subsequently transported into the cell through the GlpT transport system. Ca2+ is required for GlpQ enzymatic activity. This subfamily also includes some GP-GDEs in higher plants and their eukaryotic homologs, which show very high sequence similarities with bacterial periplasmic GP-GDEs.
Comment:The catalytic mechanism of glycerophosphodiester phosphodiesterases is based on the metal ion-dependent general acid-base reaction.
Structure:1YDY;The catalytic site of Escherichia coli periplasmic glycerophosphodiester phosphodiesterase consists of two conserved histidine residues, which serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond.
Jiyao W et al.(2023). "The conserved domain database in 2023.",