7d7p: Difference between revisions

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'''Unreleased structure'''


The entry 7d7p is ON HOLD
==Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase==
<StructureSection load='7d7p' size='340' side='right'caption='[[7d7p]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</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='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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/F2TZN0_SALR5 F2TZN0_SALR5]
<div style="background-color:#fffaf0;">
== 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.


Authors:  
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>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 7d7p" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Salpingoeca rosetta]]
[[Category: Ikuta T]]
[[Category: Nureki O]]
[[Category: Shihoya W]]
[[Category: Yamashita K]]
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