2zoi: Difference between revisions

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-{{Seed}}
-[[Image:2zoi.jpg|left|200px]]
-<!--
+==Neutron Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K==
-The line below this paragraph, containing "STRUCTURE_2zoi", creates the "Structure Box" on the page.
+<StructureSection load='2zoi' size='340' side='right'caption='[[2zoi]], [[Resolution|resolution]] 1.50&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'>[[2zoi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. The March 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOI 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">Neutron Diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
-{{STRUCTURE_2zoi|  PDB=2zoi  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zoi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zoi OCA], [https://pdbe.org/2zoi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zoi RCSB], [https://www.ebi.ac.uk/pdbsum/2zoi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zoi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
+== 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/zo/2zoi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2zoi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified approximately 87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
-===Neutron Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K===
+Low-barrier hydrogen bond in photoactive yellow protein.,Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):440-4. Epub 2009 Jan 2. PMID:19122140<ref>PMID:19122140</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19122140}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2zoi" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19122140 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19122140}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ZOI is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZOI OCA].
-==Reference==
-<ref group="xtra">PMID:19122140</ref><references group="xtra"/>
 [[Category: Halorhodospira halophila]]
-[[Category: Yamaguchi, S.]]
+[[Category: Large Structures]]
-[[Category: Chromophore]]
+[[Category: Phototropin]]
-[[Category: Lbhb]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Light sensor]]
+[[Category: Yamaguchi S]]
-[[Category: Lov]]
-[[Category: Pa]]
-[[Category: Photoreceptor]]
-[[Category: Photoreceptor protein]]
-[[Category: Receptor]]
-[[Category: Sensory transduction]]
-[[Category: Shb]]
-[[Category: Signaling protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 12:18:31 2009''