3c2w - Revision history

OCA at 06:35, 3 April 2024

OCA — Wed, 03 Apr 2024 06:35:08 GMT

←Older revision		Revision as of 06:35, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='3c2w' size='340' side='right'caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3c2w' size='340' side='right'caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>bphP, PA4117 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~287~~ "~~Bacillus aeruginosus~~" ~~(Schroeter 1872) Trevisan 1885])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3]~~ </~~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=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [https://pdbe.org/3c2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [https://www.ebi.ac.uk/pdbsum/3c2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2w 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=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [https://pdbe.org/3c2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [https://www.ebi.ac.uk/pdbsum/3c2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BPHY_PSEAE BPHY_PSEAE]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (By similarity).	+	[https://www.uniprot.org/uniprot/BPHY_PSEAE BPHY_PSEAE] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=3c2w ConSurf].		</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=3c2w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 A resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an "arm" structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.
-
-	Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.,Yang X, Kuk J, Moffat K Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14715-20. Epub 2008 Sep 17. PMID:18799746<ref>PMID:18799746</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3c2w" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Histidine kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kuk, J~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Moffat, K~~]]	+	[[Category: Kuk J]]
-	[[Category: ~~Yang, X~~]]	+	[[Category: Moffat K]]
-	[[Category: ~~Chromophore]]~~	+	[[Category: Yang X]]
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Knot structure]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Photoreceptor protein]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Sensory transduction]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:41, 27 January 2022

OCA — Thu, 27 Jan 2022 07:41:13 GMT

←Older revision		Revision as of 07:41, 27 January 2022
Line 1:		Line 1:

	==Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state==		==Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state==
-	<StructureSection load='3c2w' size='340' side='right' caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='3c2w' size='340' side='right'caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3C2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [~~http~~://pdbe.org/3c2w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3c2w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2w 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=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [https://pdbe.org/3c2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [https://www.ebi.ac.uk/pdbsum/3c2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BPHY_PSEAE BPHY_PSEAE]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (By similarity).	+	[[https://www.uniprot.org/uniprot/BPHY_PSEAE BPHY_PSEAE]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
		+	[[Category: Large Structures]]
	[[Category: Kuk, J]]		[[Category: Kuk, J]]
	[[Category: Moffat, K]]		[[Category: Moffat, K]]

OCA at 13:58, 7 November 2018

OCA — Wed, 07 Nov 2018 13:58:42 GMT

←Older revision		Revision as of 13:58, 7 November 2018
Line 1:		Line 1:
		+
	==Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state==		==Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state==
	<StructureSection load='3c2w' size='340' side='right' caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3c2w' size='340' side='right' caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://pdbe.org/3c2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://pdbe.org/3c2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/3c2w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/3c2w_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 05:24, 10 February 2016

OCA — Wed, 10 Feb 2016 05:24:47 GMT

←Older revision		Revision as of 05:24, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3c2w' size='340' side='right' caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3c2w' size='340' side='right' caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa Pseudomonas aeruginosa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C2W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 ~~Pseudomonas aeruginosa~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://pdbe.org/3c2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=3c2w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3c2w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
-	[[Category: Pseudomonas aeruginosa]]
	[[Category: Kuk, J]]		[[Category: Kuk, J]]
	[[Category: Moffat, K]]		[[Category: Moffat, K]]

OCA at 12:07, 25 December 2014

OCA — Thu, 25 Dec 2014 12:07:52 GMT

←Older revision		Revision as of 12:07, 25 December 2014
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPHY_PSEAE BPHY_PSEAE]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: Kuk, J.]]	+	[[Category: Kuk, J]]
-	[[Category: Moffat, K.]]	+	[[Category: Moffat, K]]
-	[[Category: Yang, X.]]	+	[[Category: Yang, X]]
	[[Category: Chromophore]]		[[Category: Chromophore]]
	[[Category: Kinase]]		[[Category: Kinase]]

OCA at 06:52, 10 October 2014

OCA — Fri, 10 Oct 2014 06:52:07 GMT

←Older revision		Revision as of 06:52, 10 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3c2w\| PDB=3c2w \| SCENE= }}~~	+	==Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state==
-	===Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state===	+	<StructureSection load='3c2w' size='340' side='right' caption='[[3c2w]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18799746}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3c2w]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C2W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, PA4117 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c2w RCSB], [http://www.ebi.ac.uk/pdbsum/3c2w PDBsum]</span></td></tr>
		+	</table>
		+	== 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/c2/3c2w_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 A resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an "arm" structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

-	~~==Function==~~	+	Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.,Yang X, Kuk J, Moffat K Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14715-20. Epub 2008 Sep 17. PMID:18799746<ref>PMID:18799746</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.org/uniprot/BPHY_PSEAE BPHY_PSEAE]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (~~By similarity~~).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3c2w]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:018799746</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]

OCA at 09:37, 19 June 2013

OCA — Wed, 19 Jun 2013 09:37:12 GMT

←Older revision		Revision as of 09:37, 19 June 2013
Line 1:		Line 1:
-	[[Image:3c2w.png\|left\|200px]]
-
	{{STRUCTURE_3c2w\| PDB=3c2w \| SCENE= }}		{{STRUCTURE_3c2w\| PDB=3c2w \| SCENE= }}
-
	===Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state===		===Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state===
		+	{{ABSTRACT_PUBMED_18799746}}

-	~~{{ABSTRACT_PUBMED_018799746}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/BPHY_PSEAE BPHY_PSEAE]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region (By similarity).

	==About this Structure==		==About this Structure==
Line 11:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:018799746</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018799746</ref><references group="xtra"/><references/>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]

OCA: Protected "3c2w" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:02:43 GMT

Protected "3c2w" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:02, 7 January 2013

OCA at 19:02, 7 January 2013

OCA — Mon, 07 Jan 2013 19:02:39 GMT

←Older revision		Revision as of 19:02, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3c2w.png\|left\|200px]]		[[Image:3c2w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3c2w", 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_3c2w\| PDB=3c2w \| SCENE= }}		{{STRUCTURE_3c2w\| PDB=3c2w \| SCENE= }}

	===Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state===		===Crystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state===

		+	{{ABSTRACT_PUBMED_018799746}}

	==About this Structure==		==About this Structure==
-	~~3C2W~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA].	+	[[3c2w]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:018799746</ref><references group="xtra"/>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
Line 29:		Line 26:
	[[Category: Signaling protein]]		[[Category: Signaling protein]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:45:59 2009''

OCA at 13:46, 17 February 2009

OCA — Tue, 17 Feb 2009 13:46:00 GMT

←Older revision		Revision as of 13:46, 17 February 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3c2w.~~jpg~~\|left\|200px]]	+	[[Image:3c2w.png\|left\|200px]]

	<!--		<!--
Line 14:		Line 14:

	==About this Structure==		==About this Structure==
-	3C2W is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA].	+	3C2W is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2W OCA].
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: Single protein]]
	[[Category: Kuk, J.]]		[[Category: Kuk, J.]]
	[[Category: Moffat, K.]]		[[Category: Moffat, K.]]
Line 31:		Line 30:
	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Sep 24 10~~:38:~~19 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:45:59 2009''