3umd

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Current revision (14:01, 14 March 2024) (edit) (undo)
 
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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3umd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UMD FirstGlance]. <br>
<table><tr><td colspan='2'>[[3umd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UMD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
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</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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ume|3ume]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</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=3umd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3umd OCA], [https://pdbe.org/3umd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3umd RCSB], [https://www.ebi.ac.uk/pdbsum/3umd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3umd ProSAT]</span></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=3umd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3umd OCA], [https://pdbe.org/3umd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3umd RCSB], [https://www.ebi.ac.uk/pdbsum/3umd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3umd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
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[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Visualizing the three-dimensional structures of a protein during its biological activity is key to understanding its mechanism. In general, protein structure and function are pH-dependent. Changing the pH provides new insights into the mechanisms that are involved in protein activity. Photoactive yellow protein (PYP) is a signaling protein that serves as an ideal model for time-dependent studies on light-activated proteins. Its photocycle is studied extensively under different pH conditions. However, the structures of the intermediates remain unknown until time-resolved crystallography is employed. With the newest beamline developments, a comprehensive time series of Laue data can now be collected from a single protein crystal. This allows us to vary the pH. Here we present the first structure, to our knowledge, of a short-lived protein-inhibitor complex formed in the pB state of the PYP photocycle at pH 4. A water molecule that is transiently stabilized in the chromophore active site prevents the relaxation of the chromophore back to the trans configuration. As a result, the dark-state recovery is slowed down dramatically. At pH 9, PYP stops cycling through the pB state altogether. The electrostatic environment in the chromophore-binding site is the likely reason for this altered kinetics at different pH values.
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pH dependence of the photoactive yellow protein photocycle investigated by time-resolved crystallography.,Tripathi S, Srajer V, Purwar N, Henning R, Schmidt M Biophys J. 2012 Jan 18;102(2):325-32. PMID:22339869<ref>PMID:22339869</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3umd" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Halorhodospira halophila]]
[[Category: Halorhodospira halophila]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Henning, R]]
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[[Category: Henning R]]
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[[Category: Purwar, N]]
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[[Category: Purwar N]]
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[[Category: Schmidt, M]]
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[[Category: Schmidt M]]
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[[Category: Srajer, V]]
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[[Category: Srajer V]]
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[[Category: Tripathi, S]]
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[[Category: Tripathi S]]
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[[Category: Photoreceptor]]
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[[Category: Protein binding]]
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[[Category: Signal transduction]]
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Current revision

Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 4.

PDB ID 3umd

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