Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins
The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 126.96.36.199), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 188.8.131.52) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols are major sources of carbon and phosphate. Its catalytic mechanism is based on the metal ion-dependent acid-base reaction, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 184.108.40.206). Both, GDPD related proteins and PI-PLCs, belong to the superfamily of PI-PLC-like phosphodiesterases.
Comment:The catalytic mechanism of glycerophosphodiester phosphodiesterases is based on the metal ion-dependent general acid-base reaction.
Comment:The residues essential for enzyme activities and metal binding are not conserved in glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins (SVLs) or in Neurospora crassa ankyrin repeat protein NUC-2 and homologs.
Structure:2PZ0; Based on structure evidence and site-directed mutagenesis of Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase, the catalytic site consists of two conserved histidine residues. They serve as general acid and general base in catalyzing the hydrolysis of the 3'-5' phosphodiester bond. - View structure with Cn3D
Structure:1YDY;The catalytic site of Escherichia coli periplasmic glycerophosphodiester phosphodiesterase consists of two conserved histidine residues. - View structure with Cn3D