2pr5 - Revision history

OCA at 09:11, 21 February 2024

2024-02-21T09:11:35Z

← Older revision		Revision as of 09:11, 21 February 2024
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	<StructureSection load='2pr5' size='340' side='right'caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2pr5' size='340' side='right'caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900~~]. The March 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. The March 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>~~, ~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.45Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2pr6\|2pr6]]~~</~~div~~><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~pfyP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])~~</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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [https://pdbe.org/2pr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pr5 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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [https://pdbe.org/2pr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pr5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PHOT_BACSU PHOT_BACSU]] Exhibits the same spectroscopical features and blue-light induced photochemistry as plants phototropins, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct. Although it is a positive regulator in the activation of the environmental signaling branch of the general stress transcription factor sigma-B, its precise role is undetermined.<ref>PMID:11157946</ref>		[https://www.uniprot.org/uniprot/PHOT_BACSU PHOT_BACSU] Exhibits the same spectroscopical features and blue-light induced photochemistry as plants phototropins, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct. Although it is a positive regulator in the activation of the environmental signaling branch of the general stress transcription factor sigma-B, its precise role is undetermined.<ref>PMID:11157946</ref>
	== 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=2pr5 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=2pr5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The photosensor YtvA binds flavin mononucleotide and regulates the general stress reaction in Bacillus subtilis in response to blue light illumination. It belongs to the family of light-oxygen-voltage (LOV) proteins that were first described in plant phototropins and form a subgroup of the Per-Arnt-Sim (PAS) superfamily. Here, we report the three-dimensional structure of the LOV domain of YtvA in its dark and light states. The protein assumes the global fold common to all PAS domains and dimerizes via a hydrophobic interface. Directly C-terminal to the core of the LOV domain, an alpha-helix extends into the solvent. Light absorption causes formation of a covalent bond between a conserved cysteine residue and atom C(4a) of the FMN ring, which triggers rearrangements throughout the LOV domain. Concomitantly, in the dark and light structures, the two subunits of the dimeric protein rotate relative to each other by 5 degrees . This small quaternary structural change is presumably a component of the mechanism by which the activity of YtvA is regulated in response to light. In terms of both structure and signaling mechanism, YtvA differs from plant phototropins and more closely resembles prokaryotic heme-binding PAS domains.

	Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA.,Moglich A, Moffat K J Mol Biol. 2007 Oct 12;373(1):112-26. Epub 2007 Aug 2. PMID:17764689<ref>PMID:17764689</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2pr5" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus ~~globigii migula 1900~~]]		[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Phototropin]]		[[Category: Phototropin]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Moffat, K]]		[[Category: Moffat K]]
	[[Category: Moglich, A]]		[[Category: Moglich A]]
	~~[[Category: Flavoprotein]]~~
	~~[[Category: Light-oxygen-voltage]]~~
	~~[[Category: Lov]]~~
	~~[[Category: Pa]]~~
	~~[[Category: Per-arnt-sim]]~~
	~~[[Category: Signaling protein~~]]

OCA at 15:31, 17 June 2021

2021-06-17T15:31:00Z

← Older revision		Revision as of 15:31, 17 June 2021
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	==Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)==		==Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)==
	<StructureSection load='2pr5' size='340' side='right' caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2pr5' size='340' side='right'caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. The March 2015 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. The March 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pr6\|2pr6]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [~~http~~://pdbe.org/2pr5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pr5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pr5 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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [https://pdbe.org/2pr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pr5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PHOT_BACSU PHOT_BACSU]] Exhibits the same spectroscopical features and blue-light induced photochemistry as plants phototropins, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct. Although it is a positive regulator in the activation of the environmental signaling branch of the general stress transcription factor sigma-B, its precise role is undetermined.<ref>PMID:11157946</ref>		[[https://www.uniprot.org/uniprot/PHOT_BACSU PHOT_BACSU]] Exhibits the same spectroscopical features and blue-light induced photochemistry as plants phototropins, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct. Although it is a positive regulator in the activation of the environmental signaling branch of the general stress transcription factor sigma-B, its precise role is undetermined.<ref>PMID:11157946</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pr/2pr5_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pr/2pr5_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus globigii migula 1900]]		[[Category: Bacillus globigii migula 1900]]
			[[Category: Large Structures]]
	[[Category: Phototropin]]		[[Category: Phototropin]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]

OCA at 09:31, 18 October 2017

2017-10-18T09:31:48Z

← Older revision		Revision as of 09:31, 18 October 2017
Line 1:		Line 1:

	==Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)==		==Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)==
	<StructureSection load='2pr5' size='340' side='right' caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2pr5' size='340' side='right' caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://pdbe.org/2pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://pdbe.org/2pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pr5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 09:21, 8 February 2016

2016-02-08T09:21:11Z

← Older revision		Revision as of 09:21, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pr5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:08, 10 September 2015

2015-09-10T10:08:45Z

← Older revision		Revision as of 10:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2pr5' size='340' side='right' caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='2pr5' size='340' side='right' caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. The March 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://pdbe.org/2pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2pr5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus ~~subtilis~~]]		[[Category: Bacillus globigii migula 1900]]
			[[Category: Phototropin]]
			[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Moffat, K]]		[[Category: Moffat, K]]
	[[Category: Moglich, A]]		[[Category: Moglich, A]]

OCA at 22:16, 24 December 2014

2014-12-24T22:16:44Z

← Older revision		Revision as of 22:16, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PHOT_BACSU PHOT_BACSU]] Exhibits the same spectroscopical features and blue-light induced photochemistry as plants phototropins, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct. Although it is a positive regulator in the activation of the environmental signaling branch of the general stress transcription factor sigma-B, its precise role is undetermined.<ref>PMID:11157946</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Moffat, K.]]		[[Category: Moffat, K]]
	[[Category: Moglich, A.]]		[[Category: Moglich, A]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Light-oxygen-voltage]]		[[Category: Light-oxygen-voltage]]

OCA at 18:10, 30 September 2014

2014-09-30T18:10:25Z

← Older revision		Revision as of 18:10, 30 September 2014
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	[[Image:~~2pr5~~.~~png~~\|~~left~~\|~~200px~~]]		==Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)==
			<StructureSection load='2pr5' size='340' side='right' caption='[[2pr5]], [[Resolution\|resolution]] 1.45Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PR5 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pr6\|2pr6]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pfyP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pr5 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/pr/2pr5_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 photosensor YtvA binds flavin mononucleotide and regulates the general stress reaction in Bacillus subtilis in response to blue light illumination. It belongs to the family of light-oxygen-voltage (LOV) proteins that were first described in plant phototropins and form a subgroup of the Per-Arnt-Sim (PAS) superfamily. Here, we report the three-dimensional structure of the LOV domain of YtvA in its dark and light states. The protein assumes the global fold common to all PAS domains and dimerizes via a hydrophobic interface. Directly C-terminal to the core of the LOV domain, an alpha-helix extends into the solvent. Light absorption causes formation of a covalent bond between a conserved cysteine residue and atom C(4a) of the FMN ring, which triggers rearrangements throughout the LOV domain. Concomitantly, in the dark and light structures, the two subunits of the dimeric protein rotate relative to each other by 5 degrees . This small quaternary structural change is presumably a component of the mechanism by which the activity of YtvA is regulated in response to light. In terms of both structure and signaling mechanism, YtvA differs from plant phototropins and more closely resembles prokaryotic heme-binding PAS domains.

	~~{{STRUCTURE_2pr5\| PDB=2pr5 \| SCENE= }}~~		Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA.,Moglich A, Moffat K J Mol Biol. 2007 Oct 12;373(1):112-26. Epub 2007 Aug 2. PMID:17764689<ref>PMID:17764689</ref>

	~~===Structural Basis for Light-dependent Signaling in~~ the ~~Dimeric LOV Photosensor YtvA (Dark Structure)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17764689}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2PR5 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017764689<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Moffat, K.]]		[[Category: Moffat, K.]]

OCA: Protected "2pr5" [edit=sysop:move=sysop]

2013-01-07T10:26:52Z

Protected "2pr5" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:26, 7 January 2013
(No difference)

OCA at 10:26, 7 January 2013

2013-01-07T10:26:45Z

← Older revision		Revision as of 10:26, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2pr5.png\|left\|200px]]		[[Image:2pr5.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2pr5", 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_2pr5\| PDB=2pr5 \| SCENE= }}		{{STRUCTURE_2pr5\| PDB=2pr5 \| SCENE= }}

	===Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)===		===Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17764689}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17764689 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17764689}}		{{ABSTRACT_PUBMED_17764689}}

	==About this Structure==		==About this Structure==
	~~2PR5~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA].		[[2pr5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17764689~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017764689</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Moffat, K.]]		[[Category: Moffat, K.]]
Line 33:		Line 21:
	[[Category: Per-arnt-sim]]		[[Category: Per-arnt-sim]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:56:01 2009''~~

OCA at 18:56, 16 February 2009

2009-02-16T18:56:02Z

← Older revision		Revision as of 18:56, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2PR5 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA].		2PR5 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PR5 OCA].

	==Reference==		==Reference==
	~~Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA., Moglich A, Moffat K, J Mol Biol. 2007 Oct 12;373(1):112-26. Epub 2007 Aug 2.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17764689 17764689]~~		<ref group="xtra">PMID:17764689</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	~~[[Category: Single protein]]~~
	[[Category: Moffat, K.]]		[[Category: Moffat, K.]]
	[[Category: Moglich, A.]]		[[Category: Moglich, A.]]
Line 35:		Line 34:
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 01~~:22:~~46 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:56:01 2009''