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| | <StructureSection load='7d7p' size='340' side='right'caption='[[7d7p]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='7d7p' size='340' side='right'caption='[[7d7p]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7d7p]] is a 1 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=7D7P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D7P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7d7p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salpingoeca_rosetta Salpingoeca rosetta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D7P FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.1Å</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]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7d7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7p OCA], [https://pdbe.org/7d7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d7p RCSB], [https://www.ebi.ac.uk/pdbsum/7d7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7p 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=7d7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7p OCA], [http://pdbe.org/7d7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d7p RCSB], [http://www.ebi.ac.uk/pdbsum/7d7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7p ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/F2TZN0_SALR5 F2TZN0_SALR5] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 7d7p" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 7d7p" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Proterospongia sp. atcc 50818]] | + | [[Category: Salpingoeca rosetta]] |
| - | [[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]]
| + | |
| - | [[Category: Light-dependent phosphodiesterase]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Microbial rhodopsin]]
| + | |
| Structural highlights
7d7p is a 1 chain structure with sequence from Salpingoeca rosetta. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.1Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
F2TZN0_SALR5
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O. Structural insights into the mechanism of rhodopsin phosphodiesterase. Nat Commun. 2020 Nov 5;11(1):5605. doi: 10.1038/s41467-020-19376-7. PMID:33154353 doi:http://dx.doi.org/10.1038/s41467-020-19376-7
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