1p8u: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
New page: left|200px<br /><applet load="1p8u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p8u, resolution 1.62Å" /> '''BACTERIORHODOPSIN N'...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1p8u.jpg|left|200px]]<br /><applet load="1p8u" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1p8u, resolution 1.62&Aring;" />
'''BACTERIORHODOPSIN N' INTERMEDIATE AT 1.62 A RESOLUTION'''<br />


==Overview==
==BACTERIORHODOPSIN N' INTERMEDIATE AT 1.62 A RESOLUTION==
An M intermediate of wild-type bacteriorhodopsin and an N intermediate of, the V49A mutant were accumulated in photostationary states at pH 5.6 and, 295 K, and their crystal structures determined to 1.52A and 1.62A, resolution, respectively. They appear to be M(1) and N' in the sequence, M(1)&lt;--&gt;M(2)&lt;--&gt;M'(2)&lt;--&gt;N&lt;--&gt;N'--&gt;O--&gt;BR, where M(1), M(2), and M'(2), contain an unprotonated retinal Schiff base before and after a, reorientation switch and after proton release to the extracellular, surface, while N and N' contain a reprotonated Schiff base, before and, after reprotonation of Asp96 from the cytoplasmic surface. In M(1), we, detect a cluster of three hydrogen-bonded water molecules at Asp96, not, present in the BR state. In M(2), whose structure we reported earlier, one, of these water molecules intercalates between Asp96 and Thr46. In N', the, cluster is transformed into a single-file hydrogen-bonded chain of four, water molecules that connects Asp96 to the Schiff base. We find a network, of three water molecules near residue 219 in the crystal structure of the, non-illuminated F219L mutant, where the residue replacement creates a, cavity. This suggests that the hydration of the cytoplasmic region we, observe in N' might have occurred spontaneously, beginning at an existing, water molecule as nucleus, in the cavities from residue rearrangements in, the photocycle.
<StructureSection load='1p8u' size='340' side='right'caption='[[1p8u]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1p8u]] 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=1P8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P8U 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]] 1.62&#8491;, 2 models</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LI1:1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL'>LI1</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SQU:2,10,23-TRIMETHYL-TETRACOSANE'>SQU</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=1p8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p8u OCA], [https://pdbe.org/1p8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p8u RCSB], [https://www.ebi.ac.uk/pdbsum/1p8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p8u ProSAT]</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/p8/1p8u_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=1p8u ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
An M intermediate of wild-type bacteriorhodopsin and an N intermediate of the V49A mutant were accumulated in photostationary states at pH 5.6 and 295 K, and their crystal structures determined to 1.52A and 1.62A resolution, respectively. They appear to be M(1) and N' in the sequence, M(1)&lt;--&gt;M(2)&lt;--&gt;M'(2)&lt;--&gt;N&lt;--&gt;N'--&gt;O--&gt;BR, where M(1), M(2), and M'(2) contain an unprotonated retinal Schiff base before and after a reorientation switch and after proton release to the extracellular surface, while N and N' contain a reprotonated Schiff base, before and after reprotonation of Asp96 from the cytoplasmic surface. In M(1), we detect a cluster of three hydrogen-bonded water molecules at Asp96, not present in the BR state. In M(2), whose structure we reported earlier, one of these water molecules intercalates between Asp96 and Thr46. In N', the cluster is transformed into a single-file hydrogen-bonded chain of four water molecules that connects Asp96 to the Schiff base. We find a network of three water molecules near residue 219 in the crystal structure of the non-illuminated F219L mutant, where the residue replacement creates a cavity. This suggests that the hydration of the cytoplasmic region we observe in N' might have occurred spontaneously, beginning at an existing water molecule as nucleus, in the cavities from residue rearrangements in the photocycle.


==About this Structure==
Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base.,Schobert B, Brown LS, Lanyi JK J Mol Biol. 2003 Jul 11;330(3):553-70. PMID:12842471<ref>PMID:12842471</ref>
1P8U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum] with RET, LI1 and SQU as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1P8U OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base., Schobert B, Brown LS, Lanyi JK, J Mol Biol. 2003 Jul 11;330(3):553-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12842471 12842471]
</div>
<div class="pdbe-citations 1p8u" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Halobacterium salinarum]]
[[Category: Halobacterium salinarum]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Lanyi, J.K.]]
[[Category: Lanyi JK]]
[[Category: LI1]]
[[Category: RET]]
[[Category: SQU]]
[[Category: 7-transmembrane]]
[[Category: haloarchaea]]
[[Category: ion pump]]
[[Category: lipids]]
[[Category: membrane protein]]
[[Category: merohedral twinning]]
[[Category: photoreceptor]]
[[Category: retinal protein]]
[[Category: serpentine]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:36:21 2007''
Retrieved from "https://proteopedia.org/1p8u"