2lb9: Difference between revisions

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-[[Image:2lb9.jpg|left|200px]]
-<!--
+==Refined solution structure of a cyanobacterial phytochrome gaf domain in the red light-absorbing ground state (corrected pyrrole ring planarity)==
-The line below this paragraph, containing "STRUCTURE_2lb9", creates the "Structure Box" on the page.
+<StructureSection load='2lb9' size='340' side='right'caption='[[2lb9]]' 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'>[[2lb9]] 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=2LB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LB9 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_2lb9|  PDB=2lb9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lb9 OCA], [https://pdbe.org/2lb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lb9 RCSB], [https://www.ebi.ac.uk/pdbsum/2lb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lb9 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --&gt; Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.
-===Refined solution structure of a cyanobacterial phytochrome gaf domain in the red light-absorbing ground state (corrected pyrrole ring planarity)===
+Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.,Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD J Mol Biol. 2008 Nov 7;383(2):403-13. Epub 2008 Aug 22. PMID:18762196<ref>PMID:18762196</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[2lb9]] 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=2LB9 OCA].
+<div class="pdbe-citations 2lb9" style="background-color:#fffaf0;"></div>
-[[Category: Bacteria]]
+== References ==
-[[Category: Cornilescu, C C.]]
+<references/>
-[[Category: Cornilescu, G.]]
+__TOC__
-[[Category: Markley, J L.]]
+</StructureSection>
-[[Category: Ulijasz, A T.]]
+[[Category: Large Structures]]
-[[Category: Vierstra, R D.]]
+[[Category: Cornilescu CC]]
-[[Category: Gaf domain]]
+[[Category: Cornilescu G]]
-[[Category: Kinase]]
+[[Category: Markley JL]]
-[[Category: Pcb]]
+[[Category: Ulijasz AT]]
-[[Category: Phosphoprotein]]
+[[Category: Vierstra RD]]
-[[Category: Transferase]]