2koi: Difference between revisions

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-[[Image:2koi.png|left|200px]]
-<!--
+==Refined solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state==
-The line below this paragraph, containing "STRUCTURE_2koi", creates the "Structure Box" on the page.
+<StructureSection load='2koi' size='340' side='right'caption='[[2koi]]' 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'>[[2koi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp._JA-2-3B'a(2-13) Synechococcus sp. JA-2-3B'a(2-13)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KOI 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">Solution NMR, 20 models</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene></td></tr>
-{{STRUCTURE_2koi|  PDB=2koi  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2koi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2koi OCA], [https://pdbe.org/2koi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2koi RCSB], [https://www.ebi.ac.uk/pdbsum/2koi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2koi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q2JIZ5_SYNJB Q2JIZ5_SYNJB]
+== 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/ko/2koi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2koi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red-light-absorbing, ground state (Pr) and a far-red-light-absorbing, photoactivated state (Pfr). Although the structures of several phytochromes as Pr have been determined, little is known about the structure of Pfr and how it initiates signalling. Here we describe the three-dimensional solution structure of the bilin-binding domain as Pfr, using the cyanobacterial phytochrome from Synechococcus OSB'. Contrary to predictions, light-induced rotation of the A pyrrole ring but not the D ring is the primary motion of the chromophore during photoconversion. Subsequent rearrangements within the protein then affect intradomain and interdomain contact sites within the phytochrome dimer. On the basis of our models, we propose that phytochromes act by propagating reversible light-driven conformational changes in the bilin to altered contacts between the adjacent output domains, which in most phytochromes direct differential phosphotransfer.
-===Refined solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state===
+Structural basis for the photoconversion of a phytochrome to the activated Pfr form.,Ulijasz AT, Cornilescu G, Cornilescu CC, Zhang J, Rivera M, Markley JL, Vierstra RD Nature. 2010 Jan 14;463(7278):250-4. PMID:20075921<ref>PMID:20075921</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_20075921}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2koi" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20075921 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20075921}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2koi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KOI OCA].
+[[Category: Cornilescu CC]]
+[[Category: Cornilescu G]]
-==Reference==
+[[Category: Markley JL]]
-<ref group="xtra">PMID:20075921</ref><ref group="xtra">PMID:18762196</ref><references group="xtra"/>
+[[Category: Ulijasz AT]]
-[[Category: Bacteria]]
+[[Category: Vierstra RD]]
-[[Category: Histidine kinase]]
-[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
-[[Category: Cornilescu, C C.]]
-[[Category: Cornilescu, G.]]
-[[Category: Markley, J L.]]
-[[Category: Ulijasz, A T.]]
-[[Category: Vierstra, R D.]]
-[[Category: Bacteriophytochrome]]
-[[Category: Center for eukaryotic structural genomic]]
-[[Category: Cesg]]
-[[Category: Cyanobacterial phytochrome]]
-[[Category: Gaf domain]]
-[[Category: Kinase]]
-[[Category: Pcb]]
-[[Category: Phosphoprotein]]
-[[Category: Phycocyanobilin]]
-[[Category: Phytochrome]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]