3ume: Difference between revisions

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[[~~Image~~:~~3ume~~.~~jpg~~|~~left~~|~~200px~~]]

==Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 7==

== Structural highlights ==

<table><tr><td colspan='2'>[[3ume]] is a 1 chain structure with 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=3UME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UME FirstGlance]. <br>

</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene><br>

<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3umd|3umd]]</td></tr>

<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ume FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ume OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ume RCSB], [http://www.ebi.ac.uk/pdbsum/3ume PDBsum]</span></td></tr>

<table>

== Publication Abstract from PubMed ==

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.

<!--

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>

~~The line below this paragraph~~, ~~containing "STRUCTURE_3ume"~~, ~~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_3ume| PDB=3ume | SCENE= }}~~

~~===Structure of pB intermediate~~ of ~~Photoactive yellow protein (PYP) at pH 7===~~

From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

~~<!--~~

~~The line below this paragraph, {{ABSTRACT_PUBMED_22339869}}, adds the Publication Abstract to~~ the ~~page~~

__TOC__

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22339869 is the PubMed ID number~~.

</StructureSection>

-->

~~{{ABSTRACT_PUBMED_22339869}}~~

~~==About this Structure==~~

~~[[3ume]] is a 1 chain structure with 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=3UME OCA].~~

==~~Reference~~==

<~~ref group="xtra">PMID:022339869<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Halorhodospira halophila]]

[[Category: Henning, R.]]

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@@ Line 1: / Line 1: @@
-[[Image:3ume.jpg|left|200px]]
+==Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 7==
+<StructureSection load='3ume' size='340' side='right' caption='[[3ume]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ume]] is a 1 chain structure with 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=3UME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UME FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3umd|3umd]]</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ume FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ume OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ume RCSB], [http://www.ebi.ac.uk/pdbsum/3ume PDBsum]</span></td></tr>
+<table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-<!--
+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>
-The line below this paragraph, containing "STRUCTURE_3ume", 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_3ume|  PDB=3ume  |  SCENE=  }}
-===Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 7===
+From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+</div>
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_22339869}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 22339869 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_22339869}}
-==About this Structure==
-[[3ume]] is a 1 chain structure with 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=3UME OCA].
-==Reference==
-<ref group="xtra">PMID:022339869</ref><references group="xtra"/>
 [[Category: Halorhodospira halophila]]
 [[Category: Henning, R.]]