1lsw - Revision history

OCA at 07:35, 14 February 2024

OCA — Wed, 14 Feb 2024 07:35:48 GMT

←Older revision		Revision as of 07:35, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1lsw' size='340' side='right'caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lsw' size='340' side='right'caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium~~ japonicum~~" kirchner 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1LSW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LSW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])~~</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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [https://pdbe.org/1lsw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [https://www.ebi.ac.uk/pdbsum/1lsw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lsw ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [~~http~~://pdbe.org/1lsw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lsw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lsw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~FIXL_BRAJA FIXL_BRAJA~~]~~] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.~~	+	[https://www.uniprot.org/uniprot/FIXL_BRADU FIXL_BRADU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lsw 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=1lsw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Structures of the Bradyrhizobium japonicum FixL heme domain have been determined in the absence and presence of specific ligands to elucidate the detailed features of its O2 sensing mechanism. The putative roles of spin-state and steric hindrance were evaluated by the structure determination of ferrous CO-bound BjFixLH and correlating its features with other ligand-bound structures. As found for NO-BjFixLH, no protein conformational change was observed in CO-BjFixLH, suggesting a more complicated mechanism than solely spin state or ligand sterics. To evaluate the role of oxidation state, the structure of the ferrous deoxy-BjFixLH was determined. The structure of deoxy-BjFixLH was found to be virtually identical to the structure of the ferric met-BjFixLH. The role of hydrogen bonding of substrates to a heme-pocket water was evaluated by determining the structure of BjFixLH bound to 1-methyl-imidazole that cannot form a hydrogen bond with this water. In this case, the heme-mediated conformational change was observed, limiting the potential importance of this interaction. Finally, the structure of cyanomet-BjFixLH was revisited to rule out concerns regarding the partial occupancy of the cyanide ligand in a previous structure. In the revised structure, Arg 220 was found to move into the heme pocket to form a hydrogen bond to the bound cyanide ligand. The implications of these results on FixL's sensing mechanism are discussed.
-
-	Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum.,Hao B, Isaza C, Arndt J, Soltis M, Chan MK Biochemistry. 2002 Oct 29;41(43):12952-8. PMID:12390021<ref>PMID:12390021</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lsw" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhizobacterium~~ japonicum ~~kirchner 1896~~]]	+	[[Category: Bradyrhizobium japonicum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arndt, J]]	+	[[Category: Arndt J]]
-	[[Category: Chan~~, M K~~]]	+	[[Category: Chan MK]]
-	[[Category: Hao, B]]	+	[[Category: Hao B]]
-	[[Category: Isaza, C]]	+	[[Category: Isaza C]]
-	[[Category: Soltis, M]]	+	[[Category: Soltis M]]
-	~~[[Category: Pas fold]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:01, 25 November 2020

OCA — Wed, 25 Nov 2020 08:01:56 GMT

←Older revision		Revision as of 08:01, 25 November 2020
Line 1:		Line 1:

	==Crystal structure of the ferrous BjFixL heme domain==		==Crystal structure of the ferrous BjFixL heme domain==
-	<StructureSection load='1lsw' size='340' side='right' caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1lsw' size='340' side='right'caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LSW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1LSW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://pdbe.org/1lsw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lsw ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://pdbe.org/1lsw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lsw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Rhizobacterium japonicum kirchner 1896]]		[[Category: Rhizobacterium japonicum kirchner 1896]]
		+	[[Category: Large Structures]]
	[[Category: Arndt, J]]		[[Category: Arndt, J]]
	[[Category: Chan, M K]]		[[Category: Chan, M K]]

OCA at 08:14, 31 January 2018

OCA — Wed, 31 Jan 2018 08:14:56 GMT

←Older revision		Revision as of 08:14, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of the ferrous BjFixL heme domain==		==Crystal structure of the ferrous BjFixL heme domain==
	<StructureSection load='1lsw' size='340' side='right' caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lsw' size='340' side='right' caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://pdbe.org/1lsw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw 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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://pdbe.org/1lsw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lsw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ls/1lsw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ls/1lsw_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 10:26, 8 February 2016

OCA — Mon, 08 Feb 2016 10:26:29 GMT

←Older revision		Revision as of 10:26, 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=1lsw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:39, 10 September 2015

OCA — Thu, 10 Sep 2015 10:39:20 GMT

←Older revision		Revision as of 10:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1lsw' size='340' side='right' caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lsw' size='340' side='right' caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bradyrhizobium_japonicum Bradyrhizobium~~ japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LSW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LSW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 ~~Bradyrhizobium~~ japonicum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw 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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://pdbe.org/1lsw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw 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 1lsw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradyrhizobium~~ japonicum]]	+	[[Category: Rhizobacterium japonicum kirchner 1896]]
	[[Category: Arndt, J]]		[[Category: Arndt, J]]
	[[Category: Chan, M K]]		[[Category: Chan, M K]]

OCA at 22:40, 24 December 2014

OCA — Wed, 24 Dec 2014 22:40:21 GMT

←Older revision		Revision as of 22:40, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LSW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LSW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw 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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FIXL_BRAJA FIXL_BRAJA]] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
-	[[Category: Arndt, J.]]	+	[[Category: Arndt, J]]
-	[[Category: Chan, M K.]]	+	[[Category: Chan, M K]]
-	[[Category: Hao, B.]]	+	[[Category: Hao, B]]
-	[[Category: Isaza, C.]]	+	[[Category: Isaza, C]]
-	[[Category: Soltis, M.]]	+	[[Category: Soltis, M]]
	[[Category: Pas fold]]		[[Category: Pas fold]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA: Protected "1lsw" [edit=sysop:move=sysop]

OCA — Sun, 28 Sep 2014 13:33:49 GMT

Protected "1lsw" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:33, 28 September 2014

OCA at 13:33, 28 September 2014

OCA — Sun, 28 Sep 2014 13:33:47 GMT

←Older revision		Revision as of 13:33, 28 September 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==Crystal structure of the ferrous BjFixL heme domain==
-	[[~~Image:~~1lsw.~~png~~\|~~left~~\|200px]]	+	<StructureSection load='1lsw' size='340' side='right' caption='[[1lsw]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lsw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LSW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]], [[1lsx\|1lsx]], [[1lt0\|1lt0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FixL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</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=1lsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lsw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lsw RCSB], [http://www.ebi.ac.uk/pdbsum/1lsw 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/ls/1lsw_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 ==
		+	Structures of the Bradyrhizobium japonicum FixL heme domain have been determined in the absence and presence of specific ligands to elucidate the detailed features of its O2 sensing mechanism. The putative roles of spin-state and steric hindrance were evaluated by the structure determination of ferrous CO-bound BjFixLH and correlating its features with other ligand-bound structures. As found for NO-BjFixLH, no protein conformational change was observed in CO-BjFixLH, suggesting a more complicated mechanism than solely spin state or ligand sterics. To evaluate the role of oxidation state, the structure of the ferrous deoxy-BjFixLH was determined. The structure of deoxy-BjFixLH was found to be virtually identical to the structure of the ferric met-BjFixLH. The role of hydrogen bonding of substrates to a heme-pocket water was evaluated by determining the structure of BjFixLH bound to 1-methyl-imidazole that cannot form a hydrogen bond with this water. In this case, the heme-mediated conformational change was observed, limiting the potential importance of this interaction. Finally, the structure of cyanomet-BjFixLH was revisited to rule out concerns regarding the partial occupancy of the cyanide ligand in a previous structure. In the revised structure, Arg 220 was found to move into the heme pocket to form a hydrogen bond to the bound cyanide ligand. The implications of these results on FixL's sensing mechanism are discussed.

-	<!--	+	Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum.,Hao B, Isaza C, Arndt J, Soltis M, Chan MK Biochemistry. 2002 Oct 29;41(43):12952-8. PMID:12390021<ref>PMID:12390021</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_1lsw"~~, ~~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_1lsw\| PDB=1lsw \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~ferrous BjFixL heme domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_12390021}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 12390021 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_12390021}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~1LSW is a 1 chain structure of sequence from [http:~~/~~/en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:12390021<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Arndt, J.]]		[[Category: Arndt, J.]]
Line 31:		Line 37:
	[[Category: Soltis, M.]]		[[Category: Soltis, M.]]
	[[Category: Pas fold]]		[[Category: Pas fold]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 21:19:34 2009''~~	+

OCA at 19:19, 16 February 2009

OCA — Mon, 16 Feb 2009 19:19:35 GMT

←Older revision		Revision as of 19:19, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1LSW is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA].	+	1LSW is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LSW OCA].

	==Reference==		==Reference==
-	Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum., Hao B, Isaza C, Arndt J, Soltis M, Chan MK, Biochemistry. 2002 Oct 29;41(43):12952-8. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12390021 12390021]~~	+	<ref group="xtra">PMID:12390021</ref><references group="xtra"/>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
-	[[Category: Single protein]]
	[[Category: Arndt, J.]]		[[Category: Arndt, J.]]
	[[Category: Chan, M K.]]		[[Category: Chan, M K.]]
Line 33:		Line 32:
	[[Category: Pas fold]]		[[Category: Pas fold]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 22~~:05:~~48 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:19:34 2009''

OCA at 19:05, 2 July 2008

OCA — Wed, 02 Jul 2008 19:05:56 GMT

←Older revision		Revision as of 19:05, 2 July 2008
Line 1:		Line 1:
-	[[Image:1lsw.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1lsw.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1lsw\| PDB=1lsw \| SCENE= }}		{{STRUCTURE_1lsw\| PDB=1lsw \| SCENE= }}

-	~~'''~~Crystal structure of the ferrous BjFixL heme domain~~'''~~	+	===Crystal structure of the ferrous BjFixL heme domain===


-	~~==Overview==~~	+	<!--
-	~~Structures of the Bradyrhizobium japonicum FixL heme domain have been determined in the absence and presence of specific ligands to elucidate the detailed features of its O2 sensing mechanism.~~ The putative roles of spin-state and steric hindrance were evaluated by the structure determination of ferrous CO-bound BjFixLH and correlating its features with other ligand-bound structures. As found for NO-BjFixLH, ~~no protein conformational change was observed in CO-BjFixLH~~, ~~suggesting a more complicated mechanism than solely spin state or ligand sterics. To evaluate~~ the ~~role of oxidation state, the structure of the ferrous deoxy-BjFixLH was determined. The structure of deoxy-BjFixLH was found to be virtually identical~~ to the ~~structure of the ferric met-BjFixLH~~. ~~The role of hydrogen bonding of substrates to a heme-pocket water was evaluated by determining the structure of BjFixLH bound to 1-methyl-imidazole that cannot form a hydrogen bond with this water~~. ~~In this case~~, the ~~heme-mediated conformational change was observed, limiting the potential importance of this interaction~~. ~~Finally, the structure of cyanomet~~-BjFixLH was revisited to rule out concerns regarding the partial occupancy of the cyanide ligand in a previous structure. In the revised structure, Arg 220 was found to move into the heme pocket to form a hydrogen bond to the bound cyanide ligand. The implications of these results on FixL's sensing mechanism are discussed.	+	The line below this paragraph, {{ABSTRACT_PUBMED_12390021}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 12390021 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_12390021}}

	==About this Structure==		==About this Structure==
Line 28:		Line 32:
	[[Category: Soltis, M.]]		[[Category: Soltis, M.]]
	[[Category: Pas fold]]		[[Category: Pas fold]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May~~ ~~3 00~~:15:27 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 22:05:48 2008''