2gw4: Difference between revisions

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-{{Seed}}
-[[Image:2gw4.png|left|200px]]
-<!--
+==Crystal structure of stony coral fluorescent protein Kaede, red form==
-The line below this paragraph, containing "STRUCTURE_2gw4", creates the "Structure Box" on the page.
+<StructureSection load='2gw4' size='340' side='right'caption='[[2gw4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2gw4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trachyphyllia_geoffroyi Trachyphyllia geoffroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GW4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=RC7:{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE'>RC7</scene></td></tr>
-{{STRUCTURE_2gw4|  PDB=2gw4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gw4 OCA], [https://pdbe.org/2gw4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gw4 RCSB], [https://www.ebi.ac.uk/pdbsum/2gw4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gw4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8I6J8_TRAGO Q8I6J8_TRAGO]
+== 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/gw/2gw4_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=2gw4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A coral fluorescent protein from Trachyphyllia geoffroyi, Kaede, possesses a tripeptide of His62-Tyr63-Gly64, which forms a chromophore with green fluorescence. This chromophore's fluorescence turns red following UV light irradiation. We have previously shown that such photoconversion is achieved by a formal beta-elimination reaction, which results in a cleavage of the peptide bond found between the amide nitrogen and the alpha-carbon at His62. However, the stereochemical arrangement of the chromophore and the precise structural basis for this reaction mechanism previously remained unknown. Here, we report the crystal structures of the green and red form of Kaede at 1.4 A and 1.6 A resolutions, respectively. Our structures depict the cleaved peptide bond in the red form. The chromophore conformations both in the green and red forms are similar, except a well-defined water molecule in the proximity of the His62 imidazole ring in the green form. We propose a molecular mechanism for green-to-red photoconversion, which is assisted by the water molecule.
-===Crystal structure of stony coral fluorescent protein Kaede, red form===
+Crystallographic evidence for water-assisted photo-induced peptide cleavage in the stony coral fluorescent protein Kaede.,Hayashi I, Mizuno H, Tong KI, Furuta T, Tanaka F, Yoshimura M, Miyawaki A, Ikura M J Mol Biol. 2007 Sep 28;372(4):918-26. Epub 2007 Jun 19. PMID:17692334<ref>PMID:17692334</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17692334}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2gw4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17692334 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17692334}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-GW4 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Trachyphyllia_geoffroyi Trachyphyllia geoffroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GW4 OCA].
-==Reference==
-Crystallographic evidence for water-assisted photo-induced peptide cleavage in the stony coral fluorescent protein Kaede., Hayashi I, Mizuno H, Tong KI, Furuta T, Tanaka F, Yoshimura M, Miyawaki A, Ikura M, J Mol Biol. 2007 Sep 28;372(4):918-26. Epub 2007 Jun 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17692334 17692334]
-[[Category: Protein complex]]
 [[Category: Trachyphyllia geoffroyi]]
-[[Category: Hayashi, I.]]
+[[Category: Hayashi I]]
-[[Category: Ikura, M.]]
+[[Category: Ikura M]]
-[[Category: Miyawako, A.]]
+[[Category: Miyawako A]]
-[[Category: Mizuno, H.]]
+[[Category: Mizuno H]]
-[[Category: Beta barrel]]
-[[Category: Luminescent protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:59:24 2008''