3pyp: Difference between revisions

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-{{STRUCTURE_3pyp|  PDB=3pyp  |  SCENE=  }}
-===PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE===
-{{ABSTRACT_PUBMED_9515969}}
-==About this Structure==
+==PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE==
-[[3pyp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PYP OCA].
+<StructureSection load='3pyp' size='340' side='right'caption='[[3pyp]], [[Resolution|resolution]] 0.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3pyp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PYP 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]] 0.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</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=3pyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pyp OCA], [https://pdbe.org/3pyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pyp RCSB], [https://www.ebi.ac.uk/pdbsum/3pyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pyp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/3pyp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3pyp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Protein photosensors from all kingdoms of life use bound organic molecules, known as chromophores, to detect light. A specific double bond within each chromophore is isomerized by light, triggering slower changes in the protein as a whole. The initial movements of the chromophore, which can occur in femtoseconds, are tightly constrained by the surrounding protein, making it difficult to see how isomerization can occur, be recognized, and be appropriately converted into a protein-wide structural change and biological signal. Here we report how this dilemma is resolved in the photoactive yellow protein (PYP). We trapped a key early intermediate in the light cycle of PYP at temperatures below -100 degrees C, and determined its structure at better than 1 A resolution. The 4-hydroxycinnamoyl chromophore isomerizes by flipping its thioester linkage with the protein, thus avoiding collisions resulting from large-scale movement of its aromatic ring during the initial light reaction. A protein-to-chromophore hydrogen bond that is present in both the preceding dark state and the subsequent signalling state of the photosensor breaks, forcing one of the hydrogen-bonding partners into a hydrophobic pocket. The isomerized bond is distorted into a conformation resembling that in the transition state. The resultant stored energy is used to drive the PYP light cycle. These results suggest a model for phototransduction, with implications for bacteriorhodopsin, photoactive proteins, PAS domains, and signalling proteins.
-==Reference==
+Structure at 0.85 A resolution of an early protein photocycle intermediate.,Genick UK, Soltis SM, Kuhn P, Canestrelli IL, Getzoff ED Nature. 1998 Mar 12;392(6672):206-9. PMID:9515969<ref>PMID:9515969</ref>
-<ref group="xtra">PMID:009515969</ref><ref group="xtra">PMID:011917145</ref><ref group="xtra">PMID:018754631</ref><references group="xtra"/><references/>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3pyp" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Halorhodospira halophila]]
-[[Category: Canestrelli, I L.]]
+[[Category: Large Structures]]
-[[Category: Genick, U K.]]
+[[Category: Canestrelli IL]]
-[[Category: Getzoff, E D.]]
+[[Category: Genick UK]]
-[[Category: Kuhn, P.]]
+[[Category: Getzoff ED]]
-[[Category: Soltis, S M.]]
+[[Category: Kuhn P]]
-[[Category: Light sensor for negative phototaxis]]
+[[Category: Soltis SM]]
-[[Category: Photoreceptor]]