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[[Image:1ixf.gif|left|200px]]
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{{STRUCTURE_1ixf|  PDB=1ixf  |  SCENE=  }}
'''Crystal Structure of the K intermediate of bacteriorhodopsin'''


==Crystal Structure of the K intermediate of bacteriorhodopsin==
<StructureSection load='1ixf' size='340' side='right'caption='[[1ixf]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ixf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXF 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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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=1ixf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixf OCA], [https://pdbe.org/1ixf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixf RCSB], [https://www.ebi.ac.uk/pdbsum/1ixf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixf ProSAT], [https://www.topsan.org/Proteins/RSGI/1ixf TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
== 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/ix/1ixf_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=1ixf ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacteriorhodopsin, the sole membrane protein of the purple membrane of Halobacterium salinarum, functions as a light-driven proton pump. A 3-D crystal of bacteriorhodopsin, which was prepared by the membrane fusion method, was used to investigate structural changes in the primary photoreaction. It was observed that when a frozen crystal was exposed to a low flux of X-ray radiation (5 x 10(14)photons mm(-2)), nearly half of the protein was converted into an orange species, exhibiting absorption peaks at 450 nm, 478 nm and 510 nm. The remainder retained the normal photochemical activity until Asp85 in the active site was decarboxlyated by a higher flux of X-ray radiation (10(16)photons mm(-2)). The procedure of diffraction measurement was improved so as to minimize the effects of the radiation damage and determine the true structural change associated with the primary photoreaction. Our structural model of the K intermediate indicates that the Schiff base linkage and the adjacent bonds in the polyene chain of retinal are largely twisted so that the Schiff base nitrogen atom still interacts with a water molecule located near Asp85. With respect to the other part of the protein, no appreciable displacement is induced in the primary photoreaction.


==Overview==
Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin.,Matsui Y, Sakai K, Murakami M, Shiro Y, Adachi S, Okumura H, Kouyama T J Mol Biol. 2002 Nov 29;324(3):469-81. PMID:12445782<ref>PMID:12445782</ref>
Bacteriorhodopsin, the sole membrane protein of the purple membrane of Halobacterium salinarum, functions as a light-driven proton pump. A 3-D crystal of bacteriorhodopsin, which was prepared by the membrane fusion method, was used to investigate structural changes in the primary photoreaction. It was observed that when a frozen crystal was exposed to a low flux of X-ray radiation (5 x 10(14)photons mm(-2)), nearly half of the protein was converted into an orange species, exhibiting absorption peaks at 450 nm, 478 nm and 510 nm. The remainder retained the normal photochemical activity until Asp85 in the active site was decarboxlyated by a higher flux of X-ray radiation (10(16)photons mm(-2)). The procedure of diffraction measurement was improved so as to minimize the effects of the radiation damage and determine the true structural change associated with the primary photoreaction. Our structural model of the K intermediate indicates that the Schiff base linkage and the adjacent bonds in the polyene chain of retinal are largely twisted so that the Schiff base nitrogen atom still interacts with a water molecule located near Asp85. With respect to the other part of the protein, no appreciable displacement is induced in the primary photoreaction.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1IXF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IXF OCA].
</div>
<div class="pdbe-citations 1ixf" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin., Matsui Y, Sakai K, Murakami M, Shiro Y, Adachi S, Okumura H, Kouyama T, J Mol Biol. 2002 Nov 29;324(3):469-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12445782 12445782]
*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Halobacterium salinarum]]
[[Category: Halobacterium salinarum]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Adachi, S.]]
[[Category: Adachi S]]
[[Category: Kouyama, T.]]
[[Category: Kouyama T]]
[[Category: Matsui, Y.]]
[[Category: Matsui Y]]
[[Category: Murakami, M.]]
[[Category: Murakami M]]
[[Category: Okumura, H.]]
[[Category: Okumura H]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Sakai K]]
[[Category: Sakai, K.]]
[[Category: Shiro Y]]
[[Category: Shiro, Y.]]
[[Category: 13-cis retinal]]
[[Category: 7-helice]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
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Retrieved from "https://proteopedia.org/1ixf"