4q0h - Revision history

OCA at 12:43, 1 March 2024

2024-03-01T12:43:39Z

←Older revision		Revision as of 12:43, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</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]] 1.157Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [https://pdbe.org/4q0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [https://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h 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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [https://pdbe.org/4q0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [https://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA] 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. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.		[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA] 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. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phytochromes are multidomain photoswitches that drive light perception in plants and microorganisms by coupling photoreversible isomerization of their bilin chromophore to various signaling cascades. How changes in bilin conformation affect output by these photoreceptors remains poorly resolved and might include several species-specific routes. Here, we present detailed three-dimensional models of the photosensing module (PSM), and a picture of an entire dimeric photoreceptor through structural analysis of the Deinococcus radiodurans phytochrome BphP assembled with biliverdin (BV). A 1.16 angstrom-resolution crystal structure of the bilin-binding pocket as Pr illuminated the intricate network of bilin/protein/water interactions and confirmed the protonation and ZZZssa conformation of BV. Structural and spectroscopic comparisons with the photochemically-compromised D207A mutant revealed that substitutions of Asp207 allow inclusion of cyclic porphyrins in addition to BV. A crystal structure of the entire PSM showed a head-to-head, twisted dimeric arrangement with bowed helical spines and a hairpin protrusion connecting the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) and phytochrome-specific (PHY) domains. A key conserved hairpin feature is its anti-parallel, two beta-strand stem, which we show by mutagenesis to be critical for BphP photochemistry. Single-particle electron microscopic images of the full-length BphP dimer in the dark-adapted Pr and photoactivated Pfr states revealed a large-scale reorientation of the PHY domain relative to the GAF domain, which alters the position of the downstream histidine kinase output module. Together, our data support a model whereby bilin photoisomerization alters GAF/PHY domain interactions through conformational modification of the hairpin, which regulates signaling by impacting the relationship between sister output modules.
-
-	Crystallographic and Electron Microscopic Analyses of a Bacterial Phytochrome Reveal Local and Global Rearrangements During Photoconversion.,Burgie ES, Wang T, Bussell AN, Walker JM, Li H, Vierstra RD J Biol Chem. 2014 Jul 8. pii: jbc.M114.571661. PMID:25006244<ref>PMID:25006244</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4q0h" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:39, 8 February 2023

2023-02-08T07:39:26Z

←Older revision		Revision as of 07:39, 8 February 2023
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	<StructureSection load='4q0h' size='340' side='right'caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>		<StructureSection load='4q0h' size='340' side='right'caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Deira Deira~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [https://pdbe.org/4q0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [https://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, DR_A0050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [~~http~~://pdbe.org/4q0h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] 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. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.	+	[https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA] 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. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deira]]~~	+	[[Category: Deinococcus radiodurans R1]]
-	~~[[Category: Histidine kinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Burgie~~, E S~~]]	+	[[Category: Burgie ES]]
-	[[Category: Vierstra~~, R D]]~~	+	[[Category: Vierstra RD]]
-	~~[[Category: Pas gaf]]~~	+
-	~~[[Category: Photosensor]]~~	+
-	~~[[Category: Response regulator]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:34, 17 April 2019

2019-04-17T07:34:00Z

←Older revision		Revision as of 07:34, 17 April 2019
Line 1:		Line 1:

	==Deinococcus radiodurans BphP PAS-GAF==		==Deinococcus radiodurans BphP PAS-GAF==
-	<StructureSection load='4q0h' size='340' side='right' caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>	+	<StructureSection load='4q0h' size='340' side='right'caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, DR_A0050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://pdbe.org/4q0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h ProSAT]</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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://pdbe.org/4q0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
		+	[[Category: Large Structures]]
	[[Category: Burgie, E S]]		[[Category: Burgie, E S]]
	[[Category: Vierstra, R D]]		[[Category: Vierstra, R D]]

OCA at 17:09, 4 January 2017

2017-01-04T17:09:46Z

←Older revision		Revision as of 17:09, 4 January 2017
Line 1:		Line 1:
		+
	==Deinococcus radiodurans BphP PAS-GAF==		==Deinococcus radiodurans BphP PAS-GAF==
	<StructureSection load='4q0h' size='340' side='right' caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>		<StructureSection load='4q0h' size='340' side='right' caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h 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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://pdbe.org/4q0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4q0h" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:45, 25 December 2014

2014-12-25T14:45:49Z

←Older revision		Revision as of 14:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h 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=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] 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. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
-	[[Category: Burgie, E S.]]	+	[[Category: Burgie, E S]]
-	[[Category: Vierstra, R D.]]	+	[[Category: Vierstra, R D]]
	[[Category: Pas gaf]]		[[Category: Pas gaf]]
	[[Category: Photosensor]]		[[Category: Photosensor]]
	[[Category: Response regulator]]		[[Category: Response regulator]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 10:15, 16 July 2014

2014-07-16T10:15:41Z

←Older revision		Revision as of 10:15, 16 July 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Deinococcus radiodurans BphP PAS-GAF==
		+	<StructureSection load='4q0h' size='340' side='right' caption='[[4q0h]], [[Resolution\|resolution]] 1.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4q0h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0H FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4q0i\|4q0i]], [[4q0j\|4q0j]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4q0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q0h RCSB], [http://www.ebi.ac.uk/pdbsum/4q0h PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phytochromes are multidomain photoswitches that drive light perception in plants and microorganisms by coupling photoreversible isomerization of their bilin chromophore to various signaling cascades. How changes in bilin conformation affect output by these photoreceptors remains poorly resolved and might include several species-specific routes. Here, we present detailed three-dimensional models of the photosensing module (PSM), and a picture of an entire dimeric photoreceptor through structural analysis of the Deinococcus radiodurans phytochrome BphP assembled with biliverdin (BV). A 1.16 angstrom-resolution crystal structure of the bilin-binding pocket as Pr illuminated the intricate network of bilin/protein/water interactions and confirmed the protonation and ZZZssa conformation of BV. Structural and spectroscopic comparisons with the photochemically-compromised D207A mutant revealed that substitutions of Asp207 allow inclusion of cyclic porphyrins in addition to BV. A crystal structure of the entire PSM showed a head-to-head, twisted dimeric arrangement with bowed helical spines and a hairpin protrusion connecting the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) and phytochrome-specific (PHY) domains. A key conserved hairpin feature is its anti-parallel, two beta-strand stem, which we show by mutagenesis to be critical for BphP photochemistry. Single-particle electron microscopic images of the full-length BphP dimer in the dark-adapted Pr and photoactivated Pfr states revealed a large-scale reorientation of the PHY domain relative to the GAF domain, which alters the position of the downstream histidine kinase output module. Together, our data support a model whereby bilin photoisomerization alters GAF/PHY domain interactions through conformational modification of the hairpin, which regulates signaling by impacting the relationship between sister output modules.

-	~~The entry 4q0h is ON HOLD until Paper Publication~~	+	Crystallographic and Electron Microscopic Analyses of a Bacterial Phytochrome Reveal Local and Global Rearrangements During Photoconversion.,Burgie ES, Wang T, Bussell AN, Walker JM, Li H, Vierstra RD J Biol Chem. 2014 Jul 8. pii: jbc.M114.571661. PMID:25006244<ref>PMID:25006244</ref>

-	~~Authors~~: Burgie, E.S., Vierstra, R.D.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Deinococcus radiodurans BphP PAS-GAF~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histidine kinase]]
		+	[[Category: Burgie, E S.]]
		+	[[Category: Vierstra, R D.]]
		+	[[Category: Pas gaf]]
		+	[[Category: Photosensor]]
		+	[[Category: Response regulator]]
		+	[[Category: Transferase]]

OCA at 08:11, 21 May 2014

2014-05-21T08:11:50Z

←Older revision		Revision as of 08:11, 21 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4q0h is ON HOLD	+	The entry 4q0h is ON HOLD until Paper Publication

	Authors: Burgie, E.S., Vierstra, R.D.		Authors: Burgie, E.S., Vierstra, R.D.

	Description: Deinococcus radiodurans BphP PAS-GAF		Description: Deinococcus radiodurans BphP PAS-GAF

OCA: Protected "4q0h" [edit=sysop:move=sysop]

2014-04-09T06:00:09Z

Protected "4q0h" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:00, 9 April 2014

OCA: New page: '''Unreleased structure''' The entry 4q0h is ON HOLD Authors: Burgie, E.S., Vierstra, R.D. Description: Deinococcus radiodurans BphP PAS-GAF

2014-04-09T06:00:08Z

New page: '''Unreleased structure''' The entry 4q0h is ON HOLD Authors: Burgie, E.S., Vierstra, R.D. Description: Deinococcus radiodurans BphP PAS-GAF

New page

'''Unreleased structure'''

The entry 4q0h is ON HOLD

Authors: Burgie, E.S., Vierstra, R.D.

Description: Deinococcus radiodurans BphP PAS-GAF