1q5j: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1q5j.jpg|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1q5j", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1q5j|  PDB=1q5j  |  SCENE=  }}
'''Crystal structure of bacteriorhodopsin mutant P91A crystallized from bicelles'''


==Crystal structure of bacteriorhodopsin mutant P91A crystallized from bicelles==
<StructureSection load='1q5j' size='340' side='right'caption='[[1q5j]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1q5j]] is a 2 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=1Q5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q5J 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]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1q5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5j OCA], [https://pdbe.org/1q5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q5j RCSB], [https://www.ebi.ac.uk/pdbsum/1q5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q5j 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/q5/1q5j_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=1q5j ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
One of the hallmarks of membrane protein structure is the high frequency of transmembrane helix kinks, which commonly occur at proline residues. Because the proline side chain usually precludes normal helix geometry, it is reasonable to expect that proline residues generate these kinks. We observe, however, that the three prolines in bacteriorhodopsin transmembrane helices can be changed to alanine with little structural consequences. This finding leads to a conundrum: if proline is not required for helix bending, why are prolines commonly present at bends in transmembrane helices? We propose an evolutionary hypothesis in which a mutation to proline initially induces the kink. The resulting packing defects are later repaired by further mutation, thereby locking the kink in the structure. Thus, most prolines in extant proteins can be removed without major structural consequences. We further propose that nonproline kinks are places where vestigial prolines were later removed during evolution. Consistent with this hypothesis, at 14 of 17 nonproline kinks in membrane proteins of known structure, we find prolines in homologous sequences. Our analysis allows us to predict kink positions with &gt;90% reliability. Kink prediction indicates that different G protein-coupled receptor proteins have different kink patterns and therefore different structures.


==Overview==
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors.,Yohannan S, Faham S, Yang D, Whitelegge JP, Bowie JU Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):959-63. Epub 2004 Jan 19. PMID:14732697<ref>PMID:14732697</ref>
One of the hallmarks of membrane protein structure is the high frequency of transmembrane helix kinks, which commonly occur at proline residues. Because the proline side chain usually precludes normal helix geometry, it is reasonable to expect that proline residues generate these kinks. We observe, however, that the three prolines in bacteriorhodopsin transmembrane helices can be changed to alanine with little structural consequences. This finding leads to a conundrum: if proline is not required for helix bending, why are prolines commonly present at bends in transmembrane helices? We propose an evolutionary hypothesis in which a mutation to proline initially induces the kink. The resulting packing defects are later repaired by further mutation, thereby locking the kink in the structure. Thus, most prolines in extant proteins can be removed without major structural consequences. We further propose that nonproline kinks are places where vestigial prolines were later removed during evolution. Consistent with this hypothesis, at 14 of 17 nonproline kinks in membrane proteins of known structure, we find prolines in homologous sequences. Our analysis allows us to predict kink positions with &gt;90% reliability. Kink prediction indicates that different G protein-coupled receptor proteins have different kink patterns and therefore different structures.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1Q5J 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=1Q5J OCA].
</div>
<div class="pdbe-citations 1q5j" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors., Yohannan S, Faham S, Yang D, Whitelegge JP, Bowie JU, Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):959-63. Epub 2004 Jan 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14732697 14732697]
*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Halobacterium salinarum]]
[[Category: Halobacterium salinarum]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bowie, J U.]]
[[Category: Bowie JU]]
[[Category: Faham, S.]]
[[Category: Faham S]]
[[Category: Whitelegge, J P.]]
[[Category: Whitelegge JP]]
[[Category: Yang, D.]]
[[Category: Yang D]]
[[Category: Yohannan, S.]]
[[Category: Yohannan S]]
[[Category: Alpha helix]]
[[Category: Membrane protein]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 05:53:18 2008''
Retrieved from "https://proteopedia.org/1q5j"