Glycerophosphodiester phosphodiesterase domain (IPR030395)

Short name: GP_PDE_dom

Overlapping homologous superfamilies

Domain relationships



This entry represents the GP-PDE domain.

The glycerophosphodiester phosphodiesterases (GD-PDEs) were initially characterised in bacteria, where they have functional roles for production of metabolic carbon and phosphate sources from glycerophosphodiesters and in adherence to and degradation of mammalian host-cell membranes. Mammalian GP- GDEs have been identified more recently and shown to be implicated in several physiological functions. GD-PDEs are involved in glycerol metabolism and catalyze the reaction of glycerophosphodiester and water to alcohol and sn-glycerol-3-phosphate. They display broad specificity for glycerophosphodiesters, such as glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol and bis(glycerophosphoglycerol).

The GP-PDE domain adopts the ubiquitous triosephosphate isomerase (TIM) barrel alpha/beta fold. The TIM barrel is comprised of an eight-stranded parallel beta-sheet barrel surrounded by eight alpha-helices. There is a small insertion to the conventional TIM barrel structure referred to as the GDPD-insertion (GDPD-I). The GDPD-I is comprised of beta strands, alpha-helices (H3 and H4), and 3/10 helices. Although the TIM barrel and a small insertion are unique for GP-PDE family, there are subtle differences in size and topology of each domain [PMID: 15162496, PMID: 16909422].

Some proteins known to contain a GP-PDE domain are listed below:

  • Bacterial glycerophosphoryl diester phosphodiesterase GlpQ (EC
  • Bacterial gylcerophosphoryl diester phosphodiesterase UgpQ (EC
  • Mammalian glycerophosphodiester phosphodiesterase 1 (GDE1) (EC (or MMIR16) [PMID: 12576545], an integral membrane glycoprotein that interacts with regulator of G protein signaling proteins. It hydrolyzes glycerophosphoinositols (GPIs) producing inositol and glycerol 3-phosphate.
  • Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 5 (GDPD5) (EC 3.1.-.-) (or GDE2) [PMID: 15276213].
  • Mammalian glycerophosphoinositol inositolphosphodiesterase GDPD2 (or GDE3) (EC [PMID: 12933806], up-regulated during osteoblast differentiation and can affect cell morpholgy. It hydrolyzes glycerophosphoinositol (GroPIns), producing inositol 1-phosphate and glycerol.
  • Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1) (EC 3.1.-.-) (or GDE4) [PMID: 18991142].
  • Mammalian glycerophosphocholine phosphodiesterase GPCPD1 (EC (or GDE5), selectively hydrolyzes glycerophosphocholine (GroPCho) and controls skeletal muscle development [PMID: 20576599].
  • Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 4 (GDPD4) (EC 3.1.-.-) (or GDE6) [PMID: 15276213].

GO terms

Biological Process

GO:0006629 lipid metabolic process

Molecular Function

GO:0008081 phosphoric diester hydrolase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE profiles