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| <StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]], [[Resolution|resolution]] 3.50Å' scene=''> | | <StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]], [[Resolution|resolution]] 3.50Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[7d7q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Proterospongia_sp._atcc_50818 Proterospongia sp. atcc 50818]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br> | | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7cj3|7cj3]], [[7d7p|7d7p]]</div></td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PTSG_02023 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=946362 Proterospongia sp. ATCC 50818])</td></tr>
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [https://pdbe.org/7d7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [https://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q ProSAT]</span></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [http://pdbe.org/7d7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [http://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q ProSAT]</span></td></tr> | |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 A resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 A) and PDE domain (2.1 A) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.
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| Structural insights into the mechanism of rhodopsin phosphodiesterase.,Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O Nat Commun. 2020 Nov 5;11(1):5605. doi: 10.1038/s41467-020-19376-7. PMID:33154353<ref>PMID:33154353</ref>
| | ==See Also== |
| | | *[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 7d7q" style="background-color:#fffaf0;"></div>
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| == References == | |
| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Proterospongia sp. atcc 50818]]
| | [[Category: Ikuta T]] |
| [[Category: Ikuta, T]] | | [[Category: Nureki O]] |
| [[Category: Nureki, O]] | | [[Category: Shihoya W]] |
| [[Category: Shihoya, W]] | | [[Category: Yamashita K]] |
| [[Category: Yamashita, K]] | |
| [[Category: Eight-transmembrane]]
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| [[Category: Light-dependent phosphodiesterase]]
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| [[Category: Membrane protein]]
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| [[Category: Microbial rhodopsin]]
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