Phosphodiesterase
From Proteopedia
(Difference between revisions)
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*PDE 1 | *PDE 1 | ||
| + | |||
| + | **[[4ojv]] – yPDE – yeast<br /> | ||
| + | **[[4ojx]] – yPDE + GMP<br /> | ||
| + | |||
| + | *PDE 1b or calcium/calmodulin-dependent 3’,5’-cyclic PDE | ||
**[[1taz]] – hPDE 1b catalytic domain – human<BR /> | **[[1taz]] – hPDE 1b catalytic domain – human<BR /> | ||
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**[[5b25]] - hPDE 1b catalytic domain (mutant) + inhibitor<br /> | **[[5b25]] - hPDE 1b catalytic domain (mutant) + inhibitor<br /> | ||
**[[2r8q]] - PDE 1b catalytic domain + inhibitor – ''Leishmania major''<br /> | **[[2r8q]] - PDE 1b catalytic domain + inhibitor – ''Leishmania major''<br /> | ||
| - | **[[4i15]] – PDE catalytic domain – ''Trypanosoma brucei''<br /> | ||
| - | **[[4ojv]] – yPDE – yeast<br /> | ||
| - | **[[4ojx]] – yPDE + GMP<br /> | ||
*PDE 2A or cGMP-dependent 3’,5’-cyclic PDE | *PDE 2A or cGMP-dependent 3’,5’-cyclic PDE | ||
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**[[1f0j]] – mPDE 2a regulatory domain (mutant) – mouse<BR /> | **[[1f0j]] – mPDE 2a regulatory domain (mutant) – mouse<BR /> | ||
**[[1z1l]], [[3ibj]], [[3itm]] - hPDE 2a catalytic domain<BR /> | **[[1z1l]], [[3ibj]], [[3itm]] - hPDE 2a catalytic domain<BR /> | ||
| - | **[[3itu]], [[4htx]], [[4htz]], [[4jib]], [[4d08]], [[4d09]], [[5xkm]], [[5vp0]], [[5u7l]], [[5u7k]], [[5u7j]], [[5u7i]], [[5u7d]], [[5u00]], [[5tzz]], [[5tzx]], [[5tzw]], [[5tzh]], [[5tzc]], [[5tza]], [[5tz3]] - hPDE 2a catalytic domain + inhibitor<br /> | + | **[[3itu]], [[4htx]], [[4htz]], [[4jib]], [[4d08]], [[4d09]], [[5xkm]], [[5vp0]], [[5vp1]], [[5u7l]], [[5u7k]], [[5u7j]], [[5u7i]], [[5u7d]], [[5u00]], [[5tzz]], [[5tzx]], [[5tzw]], [[5tzh]], [[5tzc]], [[5tza]], [[5tz3]], [[6ezf]], [[6c7j]], [[6c7i]], [[6c7g]], [[6c7f]], [[6c7e]], [[6c7d]], [[6b98]], [[6b97]], [[6b96]], [[4c1i]] - hPDE 2a catalytic domain + inhibitor<br /> |
*PDE 2H or RNA 2’,3’-cyclic PDE | *PDE 2H or RNA 2’,3’-cyclic PDE | ||
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**[[5ldp]], [[5ldo]], [[5ldm]], [[5ldk]] - EcPDE + nucleotide <br /> | **[[5ldp]], [[5ldo]], [[5ldm]], [[5ldk]] - EcPDE + nucleotide <br /> | ||
**[[5ldj]] - EcPDE + Pi <br /> | **[[5ldj]] - EcPDE + Pi <br /> | ||
| - | + | **[[5h7f]], [[5f7e]] - PDE core domain – ''Deinococcus radiodurans''<br /> | |
*PDE 3 | *PDE 3 | ||
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**[[1xot]] - hPDE 4b catalytic domain + drug<br /> | **[[1xot]] - hPDE 4b catalytic domain + drug<br /> | ||
**[[1tb5]], [[1ro9]], [[1ror]] - hPDE 4b catalytic domain + AMP<BR /> | **[[1tb5]], [[1ro9]], [[1ror]] - hPDE 4b catalytic domain + AMP<BR /> | ||
| - | **[[1y2h]], [[1y2j]], [[2qyl]], [[3d3p]], [[3kkt]], [[3frg]], [[3gwt]], [[3ly2]], [[3hmv]], [[3o56]], [[3o57]], [[3o0j]], [[3w5e]], [[3wd9]], [[4myq]], [[4kp6]], [[4nw7]], [[5k6j]] - hPDE 4b catalytic domain + inhibitor<br /> | + | **[[1y2h]], [[1y2j]], [[2qyl]], [[3d3p]], [[3kkt]], [[3frg]], [[3gwt]], [[3ly2]], [[3hmv]], [[3o56]], [[3o57]], [[3o0j]], [[3w5e]], [[3wd9]], [[4myq]], [[4kp6]], [[4nw7]], [[5k6j]], [[5ohj]], [[5laq]] - hPDE 4b catalytic domain + inhibitor<br /> |
**[[4x0f]] - hPDE 4b catalytic domain (mutant) + inhibitor<br /> | **[[4x0f]] - hPDE 4b catalytic domain (mutant) + inhibitor<br /> | ||
**[[3g45]] - hPDE 4b catalytic domain + modulator | **[[3g45]] - hPDE 4b catalytic domain + modulator | ||
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**[[2qym]] – hPDE 4c catalytic domain | **[[2qym]] – hPDE 4c catalytic domain | ||
| - | *PDE 4d | + | *PDE 4d or cAMP-specific 3’5’-cyclic PDE 4d, [[6fdc]], [[6f8x]], [[6f8w]], [[6f8v]], [[6f8u]], [[6f8t]], [[6f8r]], [[6f6u]], [[5wh6]], [[5wh5]], [[5lbo]] |
**[[1e9k]] - hPDE 4d5 N terminal – NMR<BR /> | **[[1e9k]] - hPDE 4d5 N terminal – NMR<BR /> | ||
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**[[3dba]] - PDE 6c cGMP-binding domain – chicken<BR /> | **[[3dba]] - PDE 6c cGMP-binding domain – chicken<BR /> | ||
| + | **[[5t4x]] - hPDE 6d δ subunit <br /> | ||
**[[3t5g]] – hPDE 6d δ subunit + GTP-binding protein RHEB<BR /> | **[[3t5g]] – hPDE 6d δ subunit + GTP-binding protein RHEB<BR /> | ||
**[[3t5i]] - hPDE 6d δ subunit + GTP-binding protein RHEB peptide<br /> | **[[3t5i]] - hPDE 6d δ subunit + GTP-binding protein RHEB peptide<br /> | ||
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**[[2ous]], [[2ouv]] - hPDE 10a2 catalytic domain (mutant) <BR /> | **[[2ous]], [[2ouv]] - hPDE 10a2 catalytic domain (mutant) <BR /> | ||
**[[2ovv]], [[2ovy]] – rPDE 10a catalytic domain + inhibitor<br /> | **[[2ovv]], [[2ovy]] – rPDE 10a catalytic domain + inhibitor<br /> | ||
| - | **[[2qyk]], [[3lxg]], [[2y0j]], [[3qpn]], [[3qpo]], [[3qpp]], [[3sn7]], [[3sni]], [[3snl]], [[3wi2]], [[4ael]], [[4ajd]], [[4ajf]], [[4ajg]], [[4ajm]], [[4ddl]], [[4fcb]], [[4fcd]], [[4heu]], [[4hf4]], [[4lkq]], [[4llj]], [[4llk]], [[4llp]], [[4llx]], [[4lm0]], [[4lm1]], [[4lm2]], [[4lm3]], [[4lm4]], [[4muw]], [[4mvh]], [[4yqh]], [[4ys7]], [[3ws8]], [[3ws9]], [[3wyk]], [[3wyl]], [[3wym]], [[4mrw]], [[4mrz]], [[ | + | **[[2qyk]], [[3lxg]], [[2y0j]], [[3qpn]], [[3qpo]], [[3qpp]], [[3sn7]], [[3sni]], [[3snl]], [[3wi2]], [[4ael]], [[4ajd]], [[4ajf]], [[4ajg]], [[4ajm]], [[4ddl]], [[4fcb]], [[4fcd]], [[4heu]], [[4hf4]], [[4lkq]], [[4llj]], [[4llk]], [[4llp]], [[4llx]], [[4lm0]], [[4lm1]], [[4lm2]], [[4lm3]], [[4lm4]], [[4muw]], [[4mvh]], [[4yqh]], [[4ys7]], [[3ws8]], [[3ws9]], [[3wyk]], [[3wyl]], [[3wym]], [[4mrw]], [[4mrz]], [[4ms0]], [[4msa]], [[4msc]], [[4mse]], [[4msh]], [[4msn]], [[5uwf]], [[5k9r]], [[5i2r]], [[5edi]], [[5edh]], [[5edg]], [[5ede]], [[5dh5]], [[5dh4]], [[5c2h]], [[5c2e]], [[5c2a]], [[5c29]], [[5c28]], [[5c1w]], [[5b4k]], [[5b4l]], [[5axq]], [[5axp]], [[4zo5]], [[4xy2]], [[4wn1]], [[4tpp]], [[4tpm]], [[4phw]], [[4p1r]], [[4p0n]], [[5xuj]], [[5xui]] - hPDE 10a catalytic domain + inhibitor<br /> |
**[[2wey]], [[3hqw]], [[3hqy]], [[3hqz]], [[3hr1]], [[3ui7]], [[3uuo]], [[4bbx]], [[4dff]] - hPDE 10a catalytic domain + schizophrenia drug<br /> | **[[2wey]], [[3hqw]], [[3hqy]], [[3hqz]], [[3hr1]], [[3ui7]], [[3uuo]], [[4bbx]], [[4dff]] - hPDE 10a catalytic domain + schizophrenia drug<br /> | ||
**[[2oun]] - hPDE 10a2 catalytic domain + AMP<BR /> | **[[2oun]] - hPDE 10a2 catalytic domain + AMP<BR /> | ||
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**[[4zkf]], [[4z0v]] - hPDE <br /> | **[[4zkf]], [[4z0v]] - hPDE <br /> | ||
**[[4z2b]] - hPDE + inhibitor <br /> | **[[4z2b]] - hPDE + inhibitor <br /> | ||
| + | |||
| + | *PDE b1 | ||
| + | |||
| + | **[[4i15]] – TbPDEb1 catalytic domain – ''Trypanosoma brucei''<br /> | ||
| + | **[[5l9h]], [[5l8y]], [[5l8c]], [[5g5v]], [[5g57]], [[5g2b]], [[4phl]] – TbPDEb1 catalytic domain + inhibitor<br /> | ||
| + | |||
| + | *PDE b2 | ||
| + | |||
| + | **[[5h2r]], [[5h2q]] – TbPDEb2 catalytic domain + inhibitor<br /> | ||
*U6 snRNA PDE | *U6 snRNA PDE | ||
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**[[1q32]] – yPDE <BR /> | **[[1q32]] – yPDE <BR /> | ||
**[[3sq3]], [[3sq5]], [[3sq7]], [[3sq8]] – yPDE (mutant) <BR /> | **[[3sq3]], [[3sq5]], [[3sq7]], [[3sq8]] – yPDE (mutant) <BR /> | ||
| - | **[[1jy1]], [[1qzq]] – | + | **[[1jy1]], [[1qzq]] – hPDE1 residues 149-608<BR /> |
**[[5inm]] - mPDE catalytic domain <br /> | **[[5inm]] - mPDE catalytic domain <br /> | ||
**[[5inn]] - mPDE catalytic domain (mutant) <br /> | **[[5inn]] - mPDE catalytic domain (mutant) <br /> | ||
**[[4f1i]], [[4fva]], [[4gew]] – PDE – ''Caenorhabditis elegans''<br /> | **[[4f1i]], [[4fva]], [[4gew]] – PDE – ''Caenorhabditis elegans''<br /> | ||
| - | **[[1mu7]] - | + | **[[1mu7]] - hPDE1 residues 149-608 (mutant) + WO4<BR /> |
| - | **[[1mu9]] - | + | **[[1mu9]] - hPDE1 residues 149-608 (mutant) + VO4<BR /> |
| - | **[[1nop]], [[1rff]], [[1rfi]], [[1rg1]], [[1rg2]], [[1rgt]] - | + | **[[1nop]], [[1rff]], [[1rfi]], [[1rg1]], [[1rg2]], [[1rgt]] - hPDE1 residues 149-608 (mutant) + DNA + topoisomerase peptide + VO4<BR /> |
| - | **[[1rgu]], [[1rh0]] - | + | **[[1rgu]], [[1rh0]] - hPDE1 residues 149-608 (mutant) + polynucleotide + neurohormone<br /> |
| - | **[[4f1h]], [[4fpv]] – | + | **[[5nwa]], [[5nw9]] – hPDE1 + DNA <br /> |
| + | **[[4f1h]], [[4fpv]] – zPDE + DNA – zebra fish<br /> | ||
**[[4gz0]], [[4gz1]], [[4gz2]], [[4puq]], [[5inq]], [[5inp]], [[5ino]], [[5inl]], [[5ink]], [[5ht2]] – mPDE catalytic domain + DNA<br /> | **[[4gz0]], [[4gz1]], [[4gz2]], [[4puq]], [[5inq]], [[5inp]], [[5ino]], [[5inl]], [[5ink]], [[5ht2]] – mPDE catalytic domain + DNA<br /> | ||
| + | **[[5tvq]] – mPDE catalytic domain + SUMO-2<br /> | ||
| + | **[[5tvp]] – mPDE catalytic domain + SUMO-2 + DNA<br /> | ||
**[[5j42]], [[5j3z]] - mPDE catalytic domain (mutant) + inhibitor<br /> | **[[5j42]], [[5j3z]] - mPDE catalytic domain (mutant) + inhibitor<br /> | ||
| - | **[[5j3s]], [[5j3p]] - | + | **[[5j3s]], [[5j3p]] - hPDE1 catalytic domain (mutant) + inhibitor<br /> |
| + | **[[6ca4]] - zPDE catalytic domain (mutant) + inhibitor <br /> | ||
*Glycerophosphodiester PDE | *Glycerophosphodiester PDE | ||
| - | **[[1o1z]] – | + | **[[1o1z]] – TmPDE – ''Thermotoga maritima''<BR /> |
**[[1t8q]], [[1ydy]] – EcPDE <BR /> | **[[1t8q]], [[1ydy]] – EcPDE <BR /> | ||
**[[1v8e]] – TtPDE – ''Thermus thermophilus''<BR /> | **[[1v8e]] – TtPDE – ''Thermus thermophilus''<BR /> | ||
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**[[1zcc]] – PDE – ''Agrobacterium tumefaciens''<BR /> | **[[1zcc]] – PDE – ''Agrobacterium tumefaciens''<BR /> | ||
**[[2o55]] – PDE – ''Galdieria sulphuraria''<BR /> | **[[2o55]] – PDE – ''Galdieria sulphuraria''<BR /> | ||
| - | **[[2oog]], [[2p76]] – | + | **[[2oog]], [[2p76]] – SaPDE – ''Staphylococcus aureus''<BR /> |
**[[2otd]] – PDE – ''Shigella flexneri''<BR /> | **[[2otd]] – PDE – ''Shigella flexneri''<BR /> | ||
**[[3ch0]] – PDE – ''Cytophaga hutchisonii''<BR /> | **[[3ch0]] – PDE – ''Cytophaga hutchisonii''<BR /> | ||
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**[[4b2o]] – BsPDE <br /> | **[[4b2o]] – BsPDE <br /> | ||
**[[4g75]], [[4g76]] – PaPDE <br /> | **[[4g75]], [[4g76]] – PaPDE <br /> | ||
| + | **[[5gz4]] – TcPDE – Taiwan cobra<br /> | ||
| + | **[[5gz5]] – TcPDE + AMP <br /> | ||
| + | **[[5xsi]] – SaPDE catalytic domain <br /> | ||
| + | **[[5xt3]] – SaPDE catalytic domain + C-di-GMP<br /> | ||
| + | **[[5xsn]] – SaPDE catalytic domain + C-di-AMP<br /> | ||
| + | **[[5xsp]] – SaPDE catalytic domain + AMP<br /> | ||
| + | **[[5vyd]] – PDE – ''Salpingoeca rosetta''<br /> | ||
| + | **[[5o7f]] – TmPDE (mutant) + GMP<br /> | ||
| + | **[[5o1u]] – TmPDE + AMP<br /> | ||
| + | **[[5o70]], [[5o4z]] – TmPDE (mutant) + AMP<br /> | ||
| + | **[[5o58]] – TmPDE (mutant) + RNA<br /> | ||
| + | |||
}} | }} | ||
== References == | == References == | ||
<references/> | <references/> | ||
[[Category:Topic Page]] | [[Category:Topic Page]] | ||
Revision as of 07:58, 20 August 2018
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3D Structures of phosphodiesterase
Updated on 20-August-2018
References
- ↑ Schermuly RT, Pullamsetti SS, Kwapiszewska G, Dumitrascu R, Tian X, Weissmann N, Ghofrani HA, Kaulen C, Dunkern T, Schudt C, Voswinckel R, Zhou J, Samidurai A, Klepetko W, Paddenberg R, Kummer W, Seeger W, Grimminger F. Phosphodiesterase 1 upregulation in pulmonary arterial hypertension: target for reverse-remodeling therapy. Circulation. 2007 May 1;115(17):2331-9. Epub 2007 Apr 16. PMID:17438150 doi:http://dx.doi.org/10.1161/CIRCULATIONAHA.106.676809
- ↑ Whalin ME, Scammell JG, Strada SJ, Thompson WJ. Phosphodiesterase II, the cGMP-activatable cyclic nucleotide phosphodiesterase, regulates cyclic AMP metabolism in PC12 cells. Mol Pharmacol. 1991 Jun;39(6):711-7. PMID:1646946
- ↑ Tilley DG, Maurice DH. Vascular smooth muscle cell phosphodiesterase (PDE) 3 and PDE4 activities and levels are regulated by cyclic AMP in vivo. Mol Pharmacol. 2002 Sep;62(3):497-506. PMID:12181425
- ↑ Morin F, Lugnier C, Kameni J, Voisin P. Expression and role of phosphodiesterase 6 in the chicken pineal gland. J Neurochem. 2001 Jul;78(1):88-99. PMID:11432976
- ↑ Redondo M, Brea J, Perez DI, Soteras I, Val C, Perez C, Morales-Garcia JA, Alonso-Gil S, Paul-Fernandez N, Martin-Alvarez R, Cadavid MI, Loza MI, Perez-Castillo A, Mengod G, Campillo NE, Martinez A, Gil C. Effect of phosphodiesterase 7 (PDE7) inhibitors in experimental autoimmune encephalomyelitis mice. Discovery of a new chemically diverse family of compounds. J Med Chem. 2012 Apr 12;55(7):3274-84. doi: 10.1021/jm201720d. Epub 2012 Mar 16. PMID:22385507 doi:http://dx.doi.org/10.1021/jm201720d
- ↑ Dong H, Osmanova V, Epstein PM, Brocke S. Phosphodiesterase 8 (PDE8) regulates chemotaxis of activated lymphocytes. Biochem Biophys Res Commun. 2006 Jun 30;345(2):713-9. Epub 2006 May 3. PMID:16696947 doi:http://dx.doi.org/10.1016/j.bbrc.2006.04.143
- ↑ Singh N, Patra S. Phosphodiesterase 9: insights from protein structure and role in therapeutics. Life Sci. 2014 Jun 13;106(1-2):1-11. doi: 10.1016/j.lfs.2014.04.007. Epub 2014, Apr 16. PMID:24746902 doi:http://dx.doi.org/10.1016/j.lfs.2014.04.007
- ↑ Qiu Y, Yanase T, Hu H, Tanaka T, Nishi Y, Liu M, Sueishi K, Sawamura T, Nawata H. Dihydrotestosterone suppresses foam cell formation and attenuates atherosclerosis development. Endocrinology. 2010 Jul;151(7):3307-16. doi: 10.1210/en.2009-1268. Epub 2010 Apr , 28. PMID:20427482 doi:http://dx.doi.org/10.1210/en.2009-1268
- ↑ Wood ER, Bledsoe R, Chai J, Daka P, Deng H, Ding Y, Harris-Gurley S, Kryn LH, Nartey E, Nichols J, Nolte RT, Prabhu N, Rise C, Sheahan T, Shotwell JB, Smith D, Tai V, Taylor JD, Tomberlin G, Wang L, Wisely B, You S, Xia B, Dickson H. The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors. J Biol Chem. 2015 Jun 8. pii: jbc.M115.653113. PMID:26055709 doi:http://dx.doi.org/10.1074/jbc.M115.653113
- ↑ Mroczek S, Krwawicz J, Kutner J, Lazniewski M, Kucinski I, Ginalski K, Dziembowski A. C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification. Genes Dev. 2012 Sep 1;26(17):1911-25. doi: 10.1101/gad.193169.112. Epub 2012 Aug , 16. PMID:22899009 doi:10.1101/gad.193169.112
- ↑ Schmidt AJ, Ryjenkov DA, Gomelsky M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J Bacteriol. 2005 Jul;187(14):4774-81. PMID:15995192 doi:http://dx.doi.org/187/14/4774
- ↑ Jin SL, Ding SL, Lin SC. Phosphodiesterase 4 and its inhibitors in inflammatory diseases. Chang Gung Med J. 2012 May-Jun;35(3):197-210. PMID:22735051
- ↑ Reffelmann T, Kloner RA. Cardiovascular effects of phosphodiesterase 5 inhibitors. Curr Pharm Des. 2006;12(27):3485-94. PMID:17017941
- ↑ Garcia AM, Redondo M, Martinez A, Gil C. Phosphodiesterase 10 inhibitors: new disease modifying drugs for Parkinson's disease? Curr Med Chem. 2014 Apr;21(10):1171-87. PMID:24372206
- ↑ Tian Y, Cui W, Huang M, Robinson H, Wan Y, Wang Y, Ke H. Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate. Biochemistry. 2014 Aug 5;53(30):4938-45. doi: 10.1021/bi500406h. Epub 2014 Jul, 22. PMID:25050706 doi:http://dx.doi.org/10.1021/bi500406h
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Michal Harel, Alexander Berchansky, Joel L. Sussman, Rick H. Cote
