PROSITE documentation PDOC51704GP-PDE domain profile
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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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | 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. |
| Title | Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution. | |
| Source | Proteins 56:167-170(2004). | |
| PubMed ID | 15162496 | |
| DOI | 10.1002/prot.20120 |
| 2 | Authors | Rao K.N. Bonanno J.B. Burley S.K. Swaminathan S. |
| Title | Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. | |
| Source | Proteins 65:514-518(2006). | |
| PubMed ID | 16909422 | |
| DOI | 10.1002/prot.21079 |
| 3 | Authors | Zheng B. Berrie C.P. Corda D. Farquhar M.G. |
| Title | GDE1/MIR16 is a glycerophosphoinositol phosphodiesterase regulated by stimulation of G protein-coupled receptors. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 100:1745-1750(2003). | |
| PubMed ID | 12576545 | |
| DOI | 10.1073/pnas.0337605100 |
| 4 | Authors | Nogusa Y. Fujioka Y. Komatsu R. Kato N. Yanaka N. |
| Title | Isolation and characterization of two serpentine membrane proteins containing glycerophosphodiester phosphodiesterase, GDE2 and GDE6. | |
| Source | Gene 337:173-179(2004). | |
| PubMed ID | 15276213 | |
| DOI | 10.1016/j.gene.2004.04.026 |
| 5 | Authors | Yanaka N. Imai Y. Kawai E. Akatsuka H. Wakimoto K. Nogusa Y. Kato N. Chiba H. Kotani E. Omori K. Sakurai N. |
| Title | Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation. | |
| Source | J. Biol. Chem. 278:43595-43602(2003). | |
| PubMed ID | 12933806 | |
| DOI | 10.1074/jbc.M302867200 |
| 6 | Authors | Chang P.A. Shao H.B. Long D.X. Sun Q. Wu Y.J. |
| Title | Isolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain. | |
| Source | Mol. Membr. Biol. 25:557-566(2008). | |
| PubMed ID | 18991142 | |
| DOI | 10.1080/09687680802537605 |
| 7 | Authors | 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. |
| Title | A novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism. | |
| Source | J. Biol. Chem. 285:27652-27663(2010). | |
| PubMed ID | 20576599 | |
| DOI | 10.1074/jbc.M110.106708 |
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