D
IPR030395

Glycerophosphodiester phosphodiesterase domain

InterPro entry
Short nameGP_PDE_dom
Overlapping
homologous
superfamilies
 

Description

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 α/β fold. 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:


 * Bacterial glycerophosphoryl diester phosphodiesterase GlpQ (EC 3.1.4.46).
 * Bacterial gylcerophosphoryl diester phosphodiesterase UgpQ (EC 3.1.4.46).
 * Mammalian glycerophosphodiester phosphodiesterase 1 (GDE1) (EC 3.1.4.44) (or MMIR16)
[3]
, 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)
[4]
.
 * Mammalian glycerophosphoinositol inositolphosphodiesterase GDPD2 (or GDE3) (EC 3.1.4.43)
[5]
, 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)
[6]
.
 * Mammalian glycerophosphocholine phosphodiesterase GPCPD1 (EC 3.1.4.2) (or GDE5), selectively hydrolyzes glycerophosphocholine (GroPCho) and controls skeletal muscle development
[7]
.
 * Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 4 (GDPD4) (EC 3.1.-.-) (or GDE6)
[4]
.

References

1.Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution. Santelli E, Schwarzenbacher R, McMullan D, Biorac T, Brinen LS, Canaves JM, Cambell J, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Proteins 56, 167-70, (2004). View articlePMID: 15162496

2.Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. Rao KN, Bonanno JB, Burley SK, Swaminathan S. Proteins 65, 514-8, (2006). View articlePMID: 16909422

3.GDE1/MIR16 is a glycerophosphoinositol phosphodiesterase regulated by stimulation of G protein-coupled receptors. Zheng B, Berrie CP, Corda D, Farquhar MG. Proc. Natl. Acad. Sci. U.S.A. 100, 1745-50, (2003). View articlePMID: 12576545

4.Isolation and characterization of two serpentine membrane proteins containing glycerophosphodiester phosphodiesterase, GDE2 and GDE6. Nogusa Y, Fujioka Y, Komatsu R, Kato N, Yanaka N. Gene 337, 173-9, (2004). View articlePMID: 15276213

5.Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation. Yanaka N, Imai Y, Kawai E, Akatsuka H, Wakimoto K, Nogusa Y, Kato N, Chiba H, Kotani E, Omori K, Sakurai N. J. Biol. Chem. 278, 43595-602, (2003). View articlePMID: 12933806

6.Isolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain. Chang PA, Shao HB, Long DX, Sun Q, Wu YJ. Mol. Membr. Biol. 25, 557-66, (2008). View articlePMID: 18991142

7.A novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism. Okazaki Y, Ohshima N, Yoshizawa I, Kamei Y, Mariggio S, Okamoto K, Maeda M, Nogusa Y, Fujioka Y, Izumi T, Ogawa Y, Shiro Y, Wada M, Kato N, Corda D, Yanaka N. J. Biol. Chem. 285, 27652-63, (2010). View articlePMID: 20576599

GO terms

cellular component

  • None

Cross References

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