2cmn - Revision history

OCA at 14:22, 13 December 2023

OCA — Wed, 13 Dec 2023 14:22:48 GMT

←Older revision		Revision as of 14:22, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2cmn' size='340' side='right'caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2cmn' size='340' side='right'caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cmn]] is a 1 chain structure with sequence from [https://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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CMN 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]] 2.3Å</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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</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~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [https://pdbe.org/2cmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [https://www.ebi.ac.uk/pdbsum/2cmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cmn 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=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [https://pdbe.org/2cmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [https://www.ebi.ac.uk/pdbsum/2cmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cmn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://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 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhizobacterium~~ japonicum ~~kirchner 1896]]~~	+	[[Category: Bradyrhizobium japonicum]]
-	~~[[Category: Histidine kinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brautigam~~, C A~~]]	+	[[Category: Brautigam CA]]
-	[[Category: Caceres~~, A I~~]]	+	[[Category: Caceres AI]]
-	[[Category: Gilles-Gonzalez, M A]]	+	[[Category: Gilles-Gonzalez M-A]]
-	[[Category: Gonzalez, C]]	+	[[Category: Gonzalez C]]
-	[[Category: Machius, M]]	+	[[Category: Machius M]]
-	[[Category: ~~Sousa, E H.~~Silva]]	+	[[Category: Silva Sousa EH]]
-	[[Category: Tomchick~~, D R]]~~	+	[[Category: Tomchick DR]]
-	~~[[Category: Inner membrane]]~~	+
-	~~[[Category: Nitrogen fixation]]~~	+
-	~~[[Category: Sensory transduction]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Two- component system~~]]	+

OCA at 07:12, 24 February 2021

OCA — Wed, 24 Feb 2021 07:12:23 GMT

←Older revision		Revision as of 07:12, 24 February 2021
Line 3:		Line 3:
	<StructureSection load='2cmn' size='340' side='right'caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2cmn' size='340' side='right'caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2CMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cmn]] is a 1 chain structure with sequence from [https://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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CMN 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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [~~http~~://pdbe.org/2cmn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2cmn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2cmn 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=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [https://pdbe.org/2cmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [https://www.ebi.ac.uk/pdbsum/2cmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cmn 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_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]]

OCA at 07:24, 3 April 2019

OCA — Wed, 03 Apr 2019 07:24:29 GMT

←Older revision		Revision as of 07:24, 3 April 2019
Line 1:		Line 1:

	==A Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor==		==A Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor==
-	<StructureSection load='2cmn' size='340' side='right' caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2cmn' size='340' side='right'caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN FirstGlance]. <br>
Line 36:		Line 36:
	[[Category: Rhizobacterium japonicum kirchner 1896]]		[[Category: Rhizobacterium japonicum kirchner 1896]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
		+	[[Category: Large Structures]]
	[[Category: Brautigam, C A]]		[[Category: Brautigam, C A]]
	[[Category: Caceres, A I]]		[[Category: Caceres, A I]]

OCA at 08:11, 23 May 2018

OCA — Wed, 23 May 2018 08:11:34 GMT

←Older revision		Revision as of 08:11, 23 May 2018
Line 1:		Line 1:
-	==A ~~PROXIMAL ARGININE RESIDUE IN THE SWITCHING MECHANISM OF THE FIXL OXYGEN SENSOR~~==	+
		+	==A Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor==
	<StructureSection load='2cmn' size='340' side='right' caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2cmn' size='340' side='right' caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://pdbe.org/2cmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn 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=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://pdbe.org/2cmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2cmn 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/cm/2cmn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/2cmn_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 18:26, 7 February 2016

OCA — Sun, 07 Feb 2016 18:26:19 GMT

←Older revision		Revision as of 18:26, 7 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=2cmn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:01, 10 September 2015

OCA — Thu, 10 Sep 2015 04:01:45 GMT

←Older revision		Revision as of 04:01, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2cmn' size='340' side='right' caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2cmn' size='340' side='right' caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN 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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn 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=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://pdbe.org/2cmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn 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 2cmn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradyrhizobium~~ japonicum]]	+	[[Category: Rhizobacterium japonicum kirchner 1896]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
	[[Category: Brautigam, C A]]		[[Category: Brautigam, C A]]

OCA at 17:25, 24 December 2014

OCA — Wed, 24 Dec 2014 17:25:01 GMT

←Older revision		Revision as of 17:25, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN 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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn 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=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn 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 32:		Line 34:
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
-	[[Category: Brautigam, C A.]]	+	[[Category: Brautigam, C A]]
-	[[Category: Caceres, A I.]]	+	[[Category: Caceres, A I]]
-	[[Category: Gilles-Gonzalez, M A.]]	+	[[Category: Gilles-Gonzalez, M A]]
-	[[Category: Gonzalez, C.]]	+	[[Category: Gonzalez, C]]
-	[[Category: Machius, M.]]	+	[[Category: Machius, M]]
-	[[Category: Sousa, E H.Silva.]]	+	[[Category: Sousa, E H.Silva]]
-	[[Category: Tomchick, D R.]]	+	[[Category: Tomchick, D R]]
	[[Category: Inner membrane]]		[[Category: Inner membrane]]
	[[Category: Nitrogen fixation]]		[[Category: Nitrogen fixation]]

OCA at 23:59, 29 September 2014

OCA — Mon, 29 Sep 2014 23:59:35 GMT

←Older revision		Revision as of 23:59, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2cmn.~~png~~\|~~left~~\|200px]]	+	==A PROXIMAL ARGININE RESIDUE IN THE SWITCHING MECHANISM OF THE FIXL OXYGEN SENSOR==
		+	<StructureSection load='2cmn' size='340' side='right' caption='[[2cmn]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2cmn]] 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=2CMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CMN 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]], [[1lsw\|1lsw]], [[1lsx\|1lsx]], [[1lt0\|1lt0]], [[1xj2\|1xj2]], [[1xj3\|1xj3]], [[1xj4\|1xj4]], [[1xj6\|1xj6]], [[1y28\|1y28]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cmn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cmn RCSB], [http://www.ebi.ac.uk/pdbsum/2cmn 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/cm/2cmn_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 ==
		+	In oxygen-sensing PAS domains, a conserved polar residue on the proximal side of the heme cofactor, usually arginine or histidine, interacts alternately with the protein in the "on-state" or the heme edge in the "off-state" but does not contact the bound ligand directly. We assessed the contributions of this residue in Bradyrhizobium japonicum FixL by determining the effects of an R206A substitution on the heme-PAS structure, ligand affinity, and regulatory capacity. The crystal structures of the unliganded forms of the R206A and wild-type BjFixL heme-PAS domains were similar, except for a more ruffled porphyrin ring in R206A BjFixL and a relaxation of the H214 residue and heme propionate 7 due to their lost interactions. The oxygen affinity of R206A BjFixL (Kd approximately 350 microM) was 2.5 times lower than that of BjFixL, and this was due to a higher off-rate constant for the R206A variant. The enzymatic activities of the unliganded "on-state" forms, either deoxy or met-R206A BjFixL, were comparable to each other and slightly lower (twofold less) than those of the corresponding BjFixL species. The most striking difference between the two proteins was in the enzymatic activities of the liganded "off-state" forms. In particular, saturation with a regulatory ligand (the Fe(III) form with cyanide) caused a >2000-fold inhibition of the BjFixL phosphorylation of BjFixJ, but a 140-fold inhibition of this catalytic activity in R206A BjFixL. Thus, in oxygen-sensing PAS domains, the interactions of polar residues with the heme edge couple the heme-binding domain to a transmitter during signal transduction.

-	~~{{STRUCTURE_2cmn\| PDB=2cmn \| SCENE= }}~~	+	A proximal arginine R206 participates in switching of the Bradyrhizobium japonicum FixL oxygen sensor.,Gilles-Gonzalez MA, Caceres AI, Sousa EH, Tomchick DR, Brautigam C, Gonzalez C, Machius M J Mol Biol. 2006 Jun 30;360(1):80-9. Epub 2006 May 11. PMID:16813836<ref>PMID:16813836</ref>

-	~~===A PROXIMAL ARGININE RESIDUE IN THE SWITCHING MECHANISM OF THE FIXL OXYGEN SENSOR===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16813836}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2cmn]] 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=2CMN OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016813836<~~/~~ref~~><~~ref group="xtra">PMID:002000090</ref><ref group="xtra">PMID:012820879</ref><references group="xtra"~~/>	+
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]

OCA at 12:27, 23 January 2013

OCA — Wed, 23 Jan 2013 12:27:12 GMT

←Older revision		Revision as of 12:27, 23 January 2013
Line 1:		Line 1:
	[[Image:2cmn.png\|left\|200px]]		[[Image:2cmn.png\|left\|200px]]

-	<!--
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-	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.
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	{{STRUCTURE_2cmn\| PDB=2cmn \| SCENE= }}		{{STRUCTURE_2cmn\| PDB=2cmn \| SCENE= }}

	===A PROXIMAL ARGININE RESIDUE IN THE SWITCHING MECHANISM OF THE FIXL OXYGEN SENSOR===		===A PROXIMAL ARGININE RESIDUE IN THE SWITCHING MECHANISM OF THE FIXL OXYGEN SENSOR===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16813836}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16813836 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16813836}}		{{ABSTRACT_PUBMED_16813836}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16813836~~</ref><ref group="xtra">PMID:~~2000090~~</ref><ref group="xtra">PMID:~~12820879~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016813836</ref><ref group="xtra">PMID:002000090</ref><ref group="xtra">PMID:012820879</ref><references group="xtra"/>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]
Line 32:		Line 21:
	[[Category: Sousa, E H.Silva.]]		[[Category: Sousa, E H.Silva.]]
	[[Category: Tomchick, D R.]]		[[Category: Tomchick, D R.]]
-	[[Category: Fixj]]
-	[[Category: Heme]]
	[[Category: Inner membrane]]		[[Category: Inner membrane]]
-	[[Category: Iron]]
-	[[Category: Kinase]]
-	[[Category: Membrane]]
-	[[Category: Metal-binding]]
	[[Category: Nitrogen fixation]]		[[Category: Nitrogen fixation]]
-	[[Category: Pas domain]]
-	[[Category: Phosphorylation]]
-	[[Category: Response regulator]]
-	[[Category: Sensor kinase]]
	[[Category: Sensory transduction]]		[[Category: Sensory transduction]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Two- component system]]		[[Category: Two- component system]]
-	[[Category: Two-component regulatory system]]

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

OCA — Mon, 14 Mar 2011 18:16:59 GMT

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

←Older revision

Revision as of 18:16, 14 March 2011