3gfx - Revision history

OCA at 09:54, 21 February 2024

OCA — Wed, 21 Feb 2024 09:54:15 GMT

←Older revision		Revision as of 09:54, 21 February 2024
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	<StructureSection load='3gfx' size='340' side='right'caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3gfx' size='340' side='right'caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Klep7 Klep7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_MGH_78578 Klebsiella pneumoniae subsp. pneumoniae MGH 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GFX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 2.4Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [https://pdbe.org/3gfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [https://www.ebi.ac.uk/pdbsum/3gfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfx 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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [https://pdbe.org/3gfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [https://www.ebi.ac.uk/pdbsum/3gfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A6T8V8_KLEP7 A6T8V8_KLEP7]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3gfx 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=3gfx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The ability to respond to light is crucial for most organisms. BLUF is a recently identified photoreceptor protein domain that senses blue light using a FAD chromophore. BLUF domains are present in various proteins from the Bacteria, Euglenozoa and Fungi. Although structures of single-domain BLUF proteins have been determined, none are available for a BLUF protein containing a functional output domain; the mechanism of light activation in this new class of photoreceptors has thus remained poorly understood. Here we report the biochemical, structural and mechanistic characterization of a full-length, active photoreceptor, BlrP1 (also known as KPN_01598), from Klebsiella pneumoniae. BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP (c-di-GMP). This ubiquitous second messenger controls motility, biofilm formation, virulence and antibiotic resistance in the Bacteria. Crystal structures of BlrP1 complexed with its substrate and metal ions involved in catalysis or in enzyme inhibition provide a detailed understanding of the mechanism of the EAL-domain c-di-GMP phosphodiesterases. These structures also sketch out a path of light activation of the phosphodiesterase output activity. Photon absorption by the BLUF domain of one subunit of the antiparallel BlrP1 homodimer activates the EAL domain of the second subunit through allosteric communication transmitted through conserved domain-domain interfaces.
-
-	Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase.,Barends TR, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I Nature. 2009 Jun 18;459(7249):1015-8. PMID:19536266<ref>PMID:19536266</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3gfx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Beta-glucosidase 3D structures\|Beta-glucosidase 3D structures]]		*[[Beta-glucosidase 3D structures\|Beta-glucosidase 3D structures]]
	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]		*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Klep7~~]]	+	[[Category: Klebsiella pneumoniae subsp. pneumoniae MGH 78578]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barends, T]]	+	[[Category: Barends T]]
-	[[Category: Beitlich, T]]	+	[[Category: Beitlich T]]
-	[[Category: Gomelsky, M]]	+	[[Category: Gomelsky M]]
-	[[Category: Griese, J]]	+	[[Category: Griese J]]
-	[[Category: Hartmann, E]]	+	[[Category: Hartmann E]]
-	[[Category: Kirienko, N]]	+	[[Category: Kirienko N]]
-	[[Category: Reinstein, J]]	+	[[Category: Reinstein J]]
-	[[Category: Ryjenkov, D]]	+	[[Category: Ryjenkov D]]
-	[[Category: Schlichting, I]]	+	[[Category: Schlichting I]]
-	[[Category: Shoeman, R]]	+	[[Category: Shoeman R]]
-	~~[[Category: Bluf-domain]]~~	+
-	~~[[Category: Eal-domain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Tim-barrel~~]]	+

OCA at 08:03, 9 March 2022

OCA — Wed, 09 Mar 2022 08:03:58 GMT

←Older revision		Revision as of 08:03, 9 March 2022
Line 1:		Line 1:

	==Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex==		==Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex==
-	<StructureSection load='3gfx' size='340' side='right' caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3gfx' size='340' side='right'caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Klep7 Klep7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klep7 Klep7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GFX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [~~http~~://pdbe.org/3gfx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gfx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfx 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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [https://pdbe.org/3gfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [https://www.ebi.ac.uk/pdbsum/3gfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gf/3gfx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gf/3gfx_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>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 3gfx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3gfx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-glucosidase 3D structures\|Beta-glucosidase 3D structures]]
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Klep7]]		[[Category: Klep7]]
		+	[[Category: Large Structures]]
	[[Category: Barends, T]]		[[Category: Barends, T]]
	[[Category: Beitlich, T]]		[[Category: Beitlich, T]]

OCA at 07:04, 1 November 2017

OCA — Wed, 01 Nov 2017 07:04:22 GMT

←Older revision		Revision as of 07:04, 1 November 2017
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klep7 Klep7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GFX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klep7 Klep7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GFX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,~~3AS~~,5S,~~7AR~~,9R,10R,~~10AS~~,12S,~~14AR~~)-3,5,10,12-~~TETRAHYDROXY~~-5,12-~~DIOXIDOOCTAHYDRO~~-2H,7H-~~DIFURO~~[3,2-D 3,2-J][1,3,7,9,2,8]~~TETRAOXADIPHOSPHACYCLODODECINE~~-2,9-~~DIYL~~]~~BIS~~(2-~~AMINO~~-1,9-~~DIHYDRO~~-6H-~~PURIN~~-6-~~ONE~~)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</td></tr>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 3gfx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3gfx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-glucosidase\|Beta-glucosidase]]
-	*[[C-di-GMP specific phosphodiesterases\|C-di-GMP specific phosphodiesterases]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:55, 5 August 2016

OCA — Fri, 05 Aug 2016 19:55:13 GMT

←Older revision		Revision as of 19:55, 5 August 2016
Line 1:		Line 1:
		+
	==Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex==		==Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex==
	<StructureSection load='3gfx' size='340' side='right' caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3gfx' size='340' side='right' caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Klebsiella_pneumoniae_subsp._pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klep7 Klep7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GFX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 ~~Klebsiella pneumoniae subsp. pneumoniae MGH 78578~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [http://www.ebi.ac.uk/pdbsum/3gfx 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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [http://pdbe.org/3gfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [http://www.ebi.ac.uk/pdbsum/3gfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gfx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=3gfx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3gfx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Klebsiella pneumoniae subsp. pneumoniae mgh 78578~~]]	+	[[Category: Klep7]]
	[[Category: Barends, T]]		[[Category: Barends, T]]
	[[Category: Beitlich, T]]		[[Category: Beitlich, T]]

OCA at 13:32, 18 December 2014

OCA — Thu, 18 Dec 2014 13:32:40 GMT

←Older revision		Revision as of 13:32, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3gfx\| PDB=3gfx \| SCENE= }}~~	+	==Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex==
-	===Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex===	+	<StructureSection load='3gfx' size='340' side='right' caption='[[3gfx]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19536266}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GFX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gfy\|3gfy]], [[3gfz\|3gfz]], [[3gg0\|3gg0]], [[3gg1\|3gg1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blrp1, KPN78578_15680, KPN_01598 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 Klebsiella pneumoniae subsp. pneumoniae MGH 78578])</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=3gfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gfx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gfx RCSB], [http://www.ebi.ac.uk/pdbsum/3gfx 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/gf/3gfx_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 ==
		+	The ability to respond to light is crucial for most organisms. BLUF is a recently identified photoreceptor protein domain that senses blue light using a FAD chromophore. BLUF domains are present in various proteins from the Bacteria, Euglenozoa and Fungi. Although structures of single-domain BLUF proteins have been determined, none are available for a BLUF protein containing a functional output domain; the mechanism of light activation in this new class of photoreceptors has thus remained poorly understood. Here we report the biochemical, structural and mechanistic characterization of a full-length, active photoreceptor, BlrP1 (also known as KPN_01598), from Klebsiella pneumoniae. BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP (c-di-GMP). This ubiquitous second messenger controls motility, biofilm formation, virulence and antibiotic resistance in the Bacteria. Crystal structures of BlrP1 complexed with its substrate and metal ions involved in catalysis or in enzyme inhibition provide a detailed understanding of the mechanism of the EAL-domain c-di-GMP phosphodiesterases. These structures also sketch out a path of light activation of the phosphodiesterase output activity. Photon absorption by the BLUF domain of one subunit of the antiparallel BlrP1 homodimer activates the EAL domain of the second subunit through allosteric communication transmitted through conserved domain-domain interfaces.

-	~~==About this~~ Structure==	+	Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase.,Barends TR, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I Nature. 2009 Jun 18;459(7249):1015-8. PMID:19536266<ref>PMID:19536266</ref>
-	~~[[3gfx]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Klebsiella_pneumoniae_subsp~~.~~_pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:019536266</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Beta-glucosidase\|Beta-glucosidase]]
		+	*[[C-di-GMP specific phosphodiesterases\|C-di-GMP specific phosphodiesterases]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Klebsiella pneumoniae subsp. pneumoniae mgh 78578]]		[[Category: Klebsiella pneumoniae subsp. pneumoniae mgh 78578]]
-	[[Category: Barends, T.]]	+	[[Category: Barends, T]]
-	[[Category: Beitlich, T.]]	+	[[Category: Beitlich, T]]
-	[[Category: Gomelsky, M.]]	+	[[Category: Gomelsky, M]]
-	[[Category: Griese, J.]]	+	[[Category: Griese, J]]
-	[[Category: Hartmann, E.]]	+	[[Category: Hartmann, E]]
-	[[Category: Kirienko, N.]]	+	[[Category: Kirienko, N]]
-	[[Category: Reinstein, J.]]	+	[[Category: Reinstein, J]]
-	[[Category: Ryjenkov, D.]]	+	[[Category: Ryjenkov, D]]
-	[[Category: Schlichting, I.]]	+	[[Category: Schlichting, I]]
-	[[Category: Shoeman, R.]]	+	[[Category: Shoeman, R]]
	[[Category: Bluf-domain]]		[[Category: Bluf-domain]]
	[[Category: Eal-domain]]		[[Category: Eal-domain]]

OCA at 15:26, 19 June 2013

OCA — Wed, 19 Jun 2013 15:26:58 GMT

←Older revision		Revision as of 15:26, 19 June 2013
Line 1:		Line 1:
-	[[Image:3gfx.png\|left\|200px]]
-
	{{STRUCTURE_3gfx\| PDB=3gfx \| SCENE= }}		{{STRUCTURE_3gfx\| PDB=3gfx \| SCENE= }}
-
	===Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex===		===Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex===
-		+	{{ABSTRACT_PUBMED_19536266}}
-	{{~~ABSTRACT_PUBMED_019536266~~}}	+

	==About this Structure==		==About this Structure==
	[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA].		[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA].
-
-	==See Also==
-	*[[C-di-GMP specific phosphodiesterases\|C-di-GMP specific phosphodiesterases]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019536266</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019536266</ref><references group="xtra"/><references/>
	[[Category: Klebsiella pneumoniae subsp. pneumoniae mgh 78578]]		[[Category: Klebsiella pneumoniae subsp. pneumoniae mgh 78578]]
	[[Category: Barends, T.]]		[[Category: Barends, T.]]

OCA at 21:52, 20 October 2012

OCA — Sat, 20 Oct 2012 21:52:19 GMT

←Older revision		Revision as of 21:52, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3gfx]] is a 2 chain structure ~~of [[C-di-GMP specific phosphodiesterases]]~~ with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA].	+	[[3gfx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_mgh_78578 Klebsiella pneumoniae subsp. pneumoniae mgh 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GFX OCA].

	==See Also==		==See Also==

OCA at 14:31, 27 July 2012

OCA — Fri, 27 Jul 2012 14:31:24 GMT

←Older revision		Revision as of 14:31, 27 July 2012
Line 1:		Line 1:
	[[Image:3gfx.png\|left\|200px]]		[[Image:3gfx.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gfx", 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_3gfx\| PDB=3gfx \| SCENE= }}		{{STRUCTURE_3gfx\| PDB=3gfx \| SCENE= }}

	===Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex===		===Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_019536266}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 019536266 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_019536266}}		{{ABSTRACT_PUBMED_019536266}}

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

OCA — Wed, 13 Jun 2012 10:41:03 GMT

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

←Older revision

Revision as of 10:41, 13 June 2012