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PROSITE documentation PDOC51704 [for PROSITE entry PS51704]

GP-PDE domain profile





Description

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 bis(glycerophosphoglycerol).

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:

  • 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].

The profile we developed covers the entire GP-PDE domain.

Last update:

February 2014 / First entry.

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Technical section

PROSITE method (with tools and information) covered by this documentation:

GP_PDE, PS51704; GP-PDE domain profile  (MATRIX)


References

1AuthorsSantelli 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.
TitleCrystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution.
SourceProteins 56:167-170(2004).
PubMed ID15162496
DOI10.1002/prot.20120

2AuthorsRao K.N. Bonanno J.B. Burley S.K. Swaminathan S.
TitleCrystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.
SourceProteins 65:514-518(2006).
PubMed ID16909422
DOI10.1002/prot.21079

3AuthorsZheng B. Berrie C.P. Corda D. Farquhar M.G.
TitleGDE1/MIR16 is a glycerophosphoinositol phosphodiesterase regulated by stimulation of G protein-coupled receptors.
SourceProc. Natl. Acad. Sci. U.S.A. 100:1745-1750(2003).
PubMed ID12576545
DOI10.1073/pnas.0337605100

4AuthorsNogusa Y. Fujioka Y. Komatsu R. Kato N. Yanaka N.
TitleIsolation and characterization of two serpentine membrane proteins containing glycerophosphodiester phosphodiesterase, GDE2 and GDE6.
SourceGene 337:173-179(2004).
PubMed ID15276213
DOI10.1016/j.gene.2004.04.026

5AuthorsYanaka N. Imai Y. Kawai E. Akatsuka H. Wakimoto K. Nogusa Y. Kato N. Chiba H. Kotani E. Omori K. Sakurai N.
TitleNovel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation.
SourceJ. Biol. Chem. 278:43595-43602(2003).
PubMed ID12933806
DOI10.1074/jbc.M302867200

6AuthorsChang P.A. Shao H.B. Long D.X. Sun Q. Wu Y.J.
TitleIsolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain.
SourceMol. Membr. Biol. 25:557-566(2008).
PubMed ID18991142
DOI10.1080/09687680802537605

7AuthorsOkazaki 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.
TitleA novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism.
SourceJ. Biol. Chem. 285:27652-27663(2010).
PubMed ID20576599
DOI10.1074/jbc.M110.106708



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