The glycerophosphodiester phosphodiesterases (GD-PDEs) were initially
characterized 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
The GP-PDE domain adopts the ubiquitous triosephosphate isomerase (TIM) barrel
α/β fold (see <PDOC00155>) (see <PDB:1ZCC>). The TIM barrel is
comprised of an eight-stranded parallel β-sheet barrel surrounded by eight
α-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 β strands, α-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 [1,2].
Some proteins known to contain a GP-PDE domain are listed below:
Mammalian glycerophosphodiester phosphodiesterase 1 (GDE1) (EC 126.96.36.199)
(or MMIR16) , an integral membrane glycoprotein that interacts with
regulator of G protein signaling proteins. It hydrolyzes
glycerophosphoinositols (GPIs) producing inositol and glycerol 3-phosphate.
PROSITE method (with tools and information) covered by this documentation:
Santelli E. Schwarzenbacher R. McMullan D. Biorac T. Brinen L.S. Canaves J.M. Cambell J. Dai X. Deacon A.M. Elsliger M.-A. Eshagi S. Floyd R. Godzik A. Grittini C. Grzechnik S.K. Jaroszewski L. Karlak C. Klock H.E. Koesema E. Kovarik J.S. Kreusch A. Kuhn P. Lesley S.A. McPhillips T.M. Miller M.D. Morse A. Moy K. Ouyang J. Page R. Quijano K. Rezezadeh F. Robb A. Sims E. Spraggon G. Stevens R.C. van den Bedem H. Velasquez J. Vincent J. von Delft F. Wang X. West B. Wolf G. Xu Q. Hodgson K.O. Wooley J. Wilson I.A.
Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution.
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