3qbg: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3qbg.jpg|left|200px]]
-<!--
+==Anion-free blue form of pharaonis halorhodopsin==
-The line below this paragraph, containing "STRUCTURE_3qbg", creates the "Structure Box" on the page.
+<StructureSection load='3qbg' size='340' side='right'caption='[[3qbg]], [[Resolution|resolution]] 1.80&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'>[[3qbg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QBG 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-{{STRUCTURE_3qbg|  PDB=3qbg  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3qbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qbg OCA], [https://pdbe.org/3qbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qbg RCSB], [https://www.ebi.ac.uk/pdbsum/3qbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qbg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BACH_NATPH BACH_NATPH] Light-driven anion pump. Binding affinity for the anions is in the order, bromide > chloride > nitrate > azide > bromate and binding is pH dependent.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Halorhodopsin from Natronomonas pharaonis (pHR) was previously crystallized into a monoclinic space group C2, and the structure of the chloride-bound purple form was determined. Here, we report the crystal structures of two chloride-free forms of pHR, that is, an O-like blue form and an M-like yellow form. When the C2 crystal was soaked in a chloride-free alkaline solution, the protein packing was largely altered and the yellow form containing all-trans retinal was generated. Upon neutralization, this yellow form was converted into the blue form. From structural comparison of the different forms of pHR, it was shown that the removal of a chloride ion from the primary binding site (site I), which is located between the retinal Schiff base and Thr126, is accompanied by such a deformation of helix C that the side chain of Thr126 moves toward helix G, leading to a significant shrinkage of site I. A large structural change is also induced in the chloride uptake pathway, where a flip motion of the side chain of Glu234 is accompanied by large movements of the surrounding aromatic residues. Irrespective of different charge distributions at the active site, there was no large difference in the structures of the yellow form and the blue form. It is shown that the yellow-to-purple transition is initiated by the entrance of one water and one HCl to the active site, where the proton and the chloride ion in HCl are transferred to the Schiff base and site I, respectively.
-===Anion-free blue form of pharaonis halorhodopsin===
+Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin.,Kanada S, Takeguchi Y, Murakami M, Ihara K, Kouyama T J Mol Biol. 2011 Oct 14;413(1):162-76. Epub 2011 Aug 16. PMID:21871461<ref>PMID:21871461</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3qbg" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3qbg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBG OCA].
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Natronomonas pharaonis]]
-[[Category: Kanada, S.]]
+[[Category: Kanada S]]
-[[Category: Kouyama, T.]]
+[[Category: Kouyama T]]
-[[Category: Ion pump]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Retinal]]