3s7q - Revision history

OCA at 12:49, 14 March 2024

OCA — Thu, 14 Mar 2024 12:49:30 GMT

←Older revision		Revision as of 12:49, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3s7q' size='340' side='right'caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3s7q' size='340' side='right'caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus~~ radiodurans~~" raj et al. 1960~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.748Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o9c\|2o9c]], [[2o9b\|2o9b]], [[1ztu\|1ztu]], [[3s7n\|3s7n]], [[3s7o\|3s7o]], [[3s7p\|3s7p]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, DR_A0050 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [https://pdbe.org/3s7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [https://www.ebi.ac.uk/pdbsum/3s7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7q 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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [https://pdbe.org/3s7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [https://www.ebi.ac.uk/pdbsum/3s7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7q 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 ==~~	+
-	Phytochrome is a multidomain dimeric red light photoreceptor that utilizes a chromophore-binding domain (CBD), a PHY domain, and an output module to induce cellular changes in response to light. A promising biotechnology tool emerged when a structure-based substitution at Asp-207 was shown to be an infrared fluorophore that uses a biologically available tetrapyrrole chromophore. We report multiple crystal structures of this D207H variant of the Deinococcus radiodurans CBD, in which His-207 is observed to form a hydrogen bond with either the tetrapyrrole A-ring oxygen or the Tyr-263 hydroxyl. Based on the implications of this duality for fluorescence properties, Y263F was introduced and shown to have stronger fluorescence than the original D207H template. Our structures are consistent with the model that the Y263F change prevents a red light-induced far-red light absorbing phytochrome chromophore configuration. With the goal of decreasing size and thereby facilitating use as a fluorescent tag in vivo, we also engineered a monomeric form of the CBD. Unexpectedly, photoconversion was observed in the monomer despite the lack of a PHY domain. This observation underscores an interplay between dimerization and the photochemical properties of phytochrome and suggests that the monomeric CBD could be used for further studies of the photocycle. The D207H substitution on its own in the monomer did not result in fluorescence, whereas Y263F did. Combined, the D207H and Y263F substitutions in the monomeric CBD lead to the brightest of our variants, designated Wisconsin infrared phytofluor (Wi-Phy).	+
-		+
-	Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein.,Auldridge ME, Satyshur KA, Anstrom DM, Forest KT J Biol Chem. 2012 Mar 2;287(10):7000-9. Epub 2011 Dec 30. PMID:22210774<ref>PMID:22210774</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3s7q" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Micrococcus~~ radiodurans ~~raj et al. 1960]]~~	+	[[Category: Deinococcus radiodurans]]
-	~~[[Category: Histidine kinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Auldridge~~, M E~~]]	+	[[Category: Auldridge ME]]
-	[[Category: Forest~~, K T~~]]	+	[[Category: Forest KT]]
-	[[Category: Satyshur~~, K A]]~~	+	[[Category: Satyshur KA]]
-	~~[[Category: Bacteriophytochrome]]~~	+
-	~~[[Category: Biliverdin]]~~	+
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Gaf]]~~	+
-	~~[[Category: Pa]]~~	+
-	~~[[Category: Photoreceptor]]~~	+
-	~~[[Category: Phytochrome~~]]	+

OCA at 10:41, 22 June 2022

OCA — Wed, 22 Jun 2022 10:41:41 GMT

←Older revision		Revision as of 10:41, 22 June 2022
Line 1:		Line 1:

	==Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain==		==Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain==
-	<StructureSection load='3s7q' size='340' side='right' caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='3s7q' size='340' side='right'caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o9c\|2o9c]], [[2o9b\|2o9b]], [[1ztu\|1ztu]], [[3s7n\|3s7n]], [[3s7o\|3s7o]], [[3s7p\|3s7p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o9c\|2o9c]], [[2o9b\|2o9b]], [[1ztu\|1ztu]], [[3s7n\|3s7n]], [[3s7o\|3s7o]], [[3s7p\|3s7p]]</div></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=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bphP, DR_A0050 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [~~http~~://pdbe.org/3s7q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s7q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7q 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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [https://pdbe.org/3s7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [https://www.ebi.ac.uk/pdbsum/3s7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7q 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 27:		Line 27:
	[[Category: Micrococcus radiodurans raj et al. 1960]]		[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
		+	[[Category: Large Structures]]
	[[Category: Auldridge, M E]]		[[Category: Auldridge, M E]]
	[[Category: Forest, K T]]		[[Category: Forest, K T]]

OCA at 12:38, 4 August 2016

OCA — Thu, 04 Aug 2016 12:38:25 GMT

←Older revision		Revision as of 12:38, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain==		==Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain==
	<StructureSection load='3s7q' size='340' side='right' caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3s7q' size='340' side='right' caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Deinococcus_radiodurans Deinococcus~~ radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o9c\|2o9c]], [[2o9b\|2o9b]], [[1ztu\|1ztu]], [[3s7n\|3s7n]], [[3s7o\|3s7o]], [[3s7p\|3s7p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o9c\|2o9c]], [[2o9b\|2o9b]], [[1ztu\|1ztu]], [[3s7n\|3s7n]], [[3s7o\|3s7o]], [[3s7p\|3s7p]]</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=1299 ~~Deinococcus~~ radiodurans])</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=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [http://www.ebi.ac.uk/pdbsum/3s7q 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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [http://pdbe.org/3s7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [http://www.ebi.ac.uk/pdbsum/3s7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s7q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3s7q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deinococcus~~ radiodurans]]	+	[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Auldridge, M E]]		[[Category: Auldridge, M E]]

OCA at 14:36, 24 December 2014

OCA — Wed, 24 Dec 2014 14:36:14 GMT

←Older revision		Revision as of 14:36, 24 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3s7q.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain==
		+	<StructureSection load='3s7q' size='340' side='right' caption='[[3s7q]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s7q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S7Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=LBW:3-[2-[(Z)-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E,4R)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBW</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o9c\|2o9c]], [[2o9b\|2o9b]], [[1ztu\|1ztu]], [[3s7n\|3s7n]], [[3s7o\|3s7o]], [[3s7p\|3s7p]]</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=1299 Deinococcus radiodurans])</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=3s7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s7q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s7q RCSB], [http://www.ebi.ac.uk/pdbsum/3s7q PDBsum]</span></td></tr>
		+	</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;">
		+	== Publication Abstract from PubMed ==
		+	Phytochrome is a multidomain dimeric red light photoreceptor that utilizes a chromophore-binding domain (CBD), a PHY domain, and an output module to induce cellular changes in response to light. A promising biotechnology tool emerged when a structure-based substitution at Asp-207 was shown to be an infrared fluorophore that uses a biologically available tetrapyrrole chromophore. We report multiple crystal structures of this D207H variant of the Deinococcus radiodurans CBD, in which His-207 is observed to form a hydrogen bond with either the tetrapyrrole A-ring oxygen or the Tyr-263 hydroxyl. Based on the implications of this duality for fluorescence properties, Y263F was introduced and shown to have stronger fluorescence than the original D207H template. Our structures are consistent with the model that the Y263F change prevents a red light-induced far-red light absorbing phytochrome chromophore configuration. With the goal of decreasing size and thereby facilitating use as a fluorescent tag in vivo, we also engineered a monomeric form of the CBD. Unexpectedly, photoconversion was observed in the monomer despite the lack of a PHY domain. This observation underscores an interplay between dimerization and the photochemical properties of phytochrome and suggests that the monomeric CBD could be used for further studies of the photocycle. The D207H substitution on its own in the monomer did not result in fluorescence, whereas Y263F did. Combined, the D207H and Y263F substitutions in the monomeric CBD lead to the brightest of our variants, designated Wisconsin infrared phytofluor (Wi-Phy).

-	~~{{STRUCTURE_3s7q\| PDB=3s7q \| SCENE= }}~~	+	Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein.,Auldridge ME, Satyshur KA, Anstrom DM, Forest KT J Biol Chem. 2012 Mar 2;287(10):7000-9. Epub 2011 Dec 30. PMID:22210774<ref>PMID:22210774</ref>

-	~~===Crystal Structure~~ of ~~a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22210774}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[3s7q]] is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA].~~	+	</StructureSection>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
-	[[Category: Auldridge, M E.]]	+	[[Category: Auldridge, M E]]
-	[[Category: Forest, K T.]]	+	[[Category: Forest, K T]]
-	[[Category: Satyshur, K A.]]	+	[[Category: Satyshur, K A]]
	[[Category: Bacteriophytochrome]]		[[Category: Bacteriophytochrome]]
	[[Category: Biliverdin]]		[[Category: Biliverdin]]

OCA at 14:32, 28 November 2012

OCA — Wed, 28 Nov 2012 14:32:09 GMT

←Older revision		Revision as of 14:32, 28 November 2012
Line 1:		Line 1:
	[[Image:3s7q.png\|left\|200px]]		[[Image:3s7q.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3s7q", 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_3s7q\| PDB=3s7q \| SCENE= }}		{{STRUCTURE_3s7q\| PDB=3s7q \| SCENE= }}

	===Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain===		===Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain===

		+	{{ABSTRACT_PUBMED_22210774}}

	==About this Structure==		==About this Structure==

OCA at 06:26, 11 January 2012

OCA — Wed, 11 Jan 2012 06:26:47 GMT

←Older revision		Revision as of 06:26, 11 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s7q.png\|left\|200px]]

-	The ~~entry 3s7q~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s7q", 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_3s7q\| PDB=3s7q \| SCENE= }}

-	~~Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.~~	+	===Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain===

-	~~Description: Crystal~~ Structure of a ~~Monomeric Infrared Fluorescent~~ Deinococcus radiodurans Bacteriophytochrome ~~chromophore binding domain~~	+
		+	==About this Structure==
		+	[[3s7q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S7Q OCA].
		+	[[Category: Deinococcus radiodurans]]
		+	[[Category: Histidine kinase]]
		+	[[Category: Auldridge, M E.]]
		+	[[Category: Forest, K T.]]
		+	[[Category: Satyshur, K A.]]
		+	[[Category: Bacteriophytochrome]]
		+	[[Category: Biliverdin]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Gaf]]
		+	[[Category: Pa]]
		+	[[Category: Photoreceptor]]
		+	[[Category: Phytochrome]]

OCA at 06:04, 5 October 2011

OCA — Wed, 05 Oct 2011 06:04:08 GMT

←Older revision		Revision as of 06:04, 5 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s7q is ON HOLD	+	The entry 3s7q is ON HOLD until Paper Publication

	Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.		Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.

	Description: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain		Description: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain

OCA at 05:37, 27 July 2011

OCA — Wed, 27 Jul 2011 05:37:25 GMT

←Older revision		Revision as of 05:37, 27 July 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s7q is ON HOLD ~~until sometime in the future~~	+	The entry 3s7q is ON HOLD

	Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.		Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.

	Description: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain		Description: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain

OCA at 05:55, 15 June 2011

OCA — Wed, 15 Jun 2011 05:55:40 GMT

←Older revision		Revision as of 05:55, 15 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s7q is ON HOLD	+	The entry 3s7q is ON HOLD until sometime in the future

	Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.		Authors: Auldridge, M.E., Satyshur, K.A., Forest, K.T.

	Description: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain		Description: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain

OCA: Protected "3s7q" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2011 05:29:22 GMT

Protected "3s7q" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:29, 1 June 2011