4i2o - Revision history

OCA at 11:48, 1 March 2024

2024-03-01T11:48:57Z

←Older revision		Revision as of 11:48, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I2O FirstGlance]. <br>		<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I2O FirstGlance]. <br>
-	</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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [https://pdbe.org/4i2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [https://www.ebi.ac.uk/pdbsum/4i2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i2o ProSAT]</span></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]] 1.77Å</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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [https://pdbe.org/4i2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [https://www.ebi.ac.uk/pdbsum/4i2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i2o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/O69245_BRAJP O69245_BRAJP]		[https://www.uniprot.org/uniprot/O69245_BRAJP O69245_BRAJP]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	FixK2 is a regulatory protein that activates a large number of genes for the anoxic and microoxic, endosymbiotic, and nitrogen-fixing life styles of the alpha-proteobacterium Bradyrhizobium japonicum. FixK2 belongs to the cAMP receptor protein (CRP) superfamily. Although most CRP family members are coregulated by effector molecules, the activity of FixK2 is negatively controlled by oxidation of its single cysteine (Cys-183) located next to the DNA-binding domain and possibly also by proteolysis. Here, we report the three-dimensional x-ray structure of FixK2, a representative of the FixK subgroup of the CRP superfamily. Crystallization succeeded only when (i) an oxidation- and protease-insensitive protein variant (FixK2(C183S)-His6) was used in which Cys-183 was replaced with serine and the C terminus was fused with a hexahistidine tag and (ii) this protein was allowed to form a complex with a 30-mer double-stranded target DNA. The structure of the FixK2-DNA complex was solved at a resolution of 1.77 A, at which the protein formed a homodimer. The precise protein-DNA contacts were identified, which led to an affirmation of the canonical target sequence, the so-called FixK2 box. The C terminus is surface-exposed, which might explain its sensitivity to specific cleavage and degradation. The oxidation-sensitive Cys-183 is also surface-exposed and in close proximity to DNA. Therefore, we propose a mechanism whereby the oxo acids generated after oxidation of the cysteine thiol cause an electrostatic repulsion, thus preventing specific DNA binding.
-
-	The Structure of Bradyrhizobium japonicum Transcription Factor FixK2 Unveils Sites of DNA Binding and Oxidation.,Bonnet M, Kurz M, Mesa S, Briand C, Hennecke H, Grutter MG J Biol Chem. 2013 May 17;288(20):14238-46. doi: 10.1074/jbc.M113.465484. Epub, 2013 Apr 1. PMID:23546876<ref>PMID:23546876</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4i2o" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:36, 9 November 2022

2022-11-09T08:36:43Z

←Older revision		Revision as of 08:36, 9 November 2022
Line 1:		Line 1:

	==The Structure of FixK2 from Bradyrhizobium japonicum==		==The Structure of FixK2 from Bradyrhizobium japonicum==
-	<StructureSection load='4i2o' size='340' side='right' caption='[[4i2o]], [[Resolution\|resolution]] 1.77Å' scene=''>	+	<StructureSection load='4i2o' size='340' side='right'caption='[[4i2o]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I2O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I2O FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fixK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>	+	</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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [https://pdbe.org/4i2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [https://www.ebi.ac.uk/pdbsum/4i2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i2o ProSAT]</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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [~~http~~://pdbe.org/4i2o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i2o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i2o ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O69245_BRAJP O69245_BRAJP]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhizobacterium~~ japonicum ~~kirchner 1896~~]]	+	[[Category: Bradyrhizobium japonicum]]
-	[[Category: Bonnet, M]]	+	[[Category: Large Structures]]
-	[[Category: Briand, C]]	+	[[Category: Bonnet M]]
-	[[Category: Gruetter~~, M G~~]]	+	[[Category: Briand C]]
-	[[Category: Hennecke, H]]	+	[[Category: Gruetter MG]]
-	[[Category: Kurz, M]]	+	[[Category: Hennecke H]]
-	[[Category: Mesa, S]]	+	[[Category: Kurz M]]
-	~~[[Category: Crp/fnr superfamily]]~~	+	[[Category: Mesa S]]
-	~~[[Category: Transcription regulator-dna complex~~]]	+

OCA at 18:56, 4 August 2016

2016-08-04T18:56:30Z

←Older revision		Revision as of 18:56, 4 August 2016
Line 1:		Line 1:
		+
	==The Structure of FixK2 from Bradyrhizobium japonicum==		==The Structure of FixK2 from Bradyrhizobium japonicum==
	<StructureSection load='4i2o' size='340' side='right' caption='[[4i2o]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='4i2o' size='340' side='right' caption='[[4i2o]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I2O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I2O FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fixK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 ~~Bradyrhizobium~~ japonicum])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fixK2 ([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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [http://www.ebi.ac.uk/pdbsum/4i2o 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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [http://pdbe.org/4i2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [http://www.ebi.ac.uk/pdbsum/4i2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i2o ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4i2o" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradyrhizobium~~ japonicum]]	+	[[Category: Rhizobacterium japonicum kirchner 1896]]
	[[Category: Bonnet, M]]		[[Category: Bonnet, M]]
	[[Category: Briand, C]]		[[Category: Briand, C]]

OCA at 13:09, 21 December 2014

2014-12-21T13:09:19Z

←Older revision		Revision as of 13:09, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4i2o\| PDB~~=4i2o \| ~~SCENE~~= }}	+	==The Structure of FixK2 from Bradyrhizobium japonicum==
-	===~~The Structure of FixK2~~ from Bradyrhizobium japonicum===	+	<StructureSection load='4i2o' size='340' side='right' caption='[[4i2o]], [[Resolution\|resolution]] 1.77Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23546876}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i2o]] is a 4 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=4I2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I2O FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fixK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</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=4i2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i2o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i2o RCSB], [http://www.ebi.ac.uk/pdbsum/4i2o PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	FixK2 is a regulatory protein that activates a large number of genes for the anoxic and microoxic, endosymbiotic, and nitrogen-fixing life styles of the alpha-proteobacterium Bradyrhizobium japonicum. FixK2 belongs to the cAMP receptor protein (CRP) superfamily. Although most CRP family members are coregulated by effector molecules, the activity of FixK2 is negatively controlled by oxidation of its single cysteine (Cys-183) located next to the DNA-binding domain and possibly also by proteolysis. Here, we report the three-dimensional x-ray structure of FixK2, a representative of the FixK subgroup of the CRP superfamily. Crystallization succeeded only when (i) an oxidation- and protease-insensitive protein variant (FixK2(C183S)-His6) was used in which Cys-183 was replaced with serine and the C terminus was fused with a hexahistidine tag and (ii) this protein was allowed to form a complex with a 30-mer double-stranded target DNA. The structure of the FixK2-DNA complex was solved at a resolution of 1.77 A, at which the protein formed a homodimer. The precise protein-DNA contacts were identified, which led to an affirmation of the canonical target sequence, the so-called FixK2 box. The C terminus is surface-exposed, which might explain its sensitivity to specific cleavage and degradation. The oxidation-sensitive Cys-183 is also surface-exposed and in close proximity to DNA. Therefore, we propose a mechanism whereby the oxo acids generated after oxidation of the cysteine thiol cause an electrostatic repulsion, thus preventing specific DNA binding.

-	~~==About this~~ Structure==	+	The Structure of Bradyrhizobium japonicum Transcription Factor FixK2 Unveils Sites of DNA Binding and Oxidation.,Bonnet M, Kurz M, Mesa S, Briand C, Hennecke H, Grutter MG J Biol Chem. 2013 May 17;288(20):14238-46. doi: 10.1074/jbc.M113.465484. Epub, 2013 Apr 1. PMID:23546876<ref>PMID:23546876</ref>
-	~~[[4i2o]] is a 4 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=4I2O OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023546876</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
-	[[Category: Bonnet, M.]]	+	[[Category: Bonnet, M]]
-	[[Category: Briand, C.]]	+	[[Category: Briand, C]]
-	[[Category: Gruetter, M G.]]	+	[[Category: Gruetter, M G]]
-	[[Category: Hennecke, H.]]	+	[[Category: Hennecke, H]]
-	[[Category: Kurz, M.]]	+	[[Category: Kurz, M]]
-	[[Category: Mesa, S.]]	+	[[Category: Mesa, S]]
	[[Category: Crp/fnr superfamily]]		[[Category: Crp/fnr superfamily]]
	[[Category: Transcription regulator-dna complex]]		[[Category: Transcription regulator-dna complex]]

OCA at 16:10, 19 June 2013

2013-06-19T16:10:00Z

←Older revision		Revision as of 16:10, 19 June 2013
Line 1:		Line 1:
	{{STRUCTURE_4i2o\| PDB=4i2o \| SCENE= }}		{{STRUCTURE_4i2o\| PDB=4i2o \| SCENE= }}
	===The Structure of FixK2 from Bradyrhizobium japonicum===		===The Structure of FixK2 from Bradyrhizobium japonicum===
		+	{{ABSTRACT_PUBMED_23546876}}

	==About this Structure==		==About this Structure==
	[[4i2o]] is a 4 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=4I2O OCA].		[[4i2o]] is a 4 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=4I2O OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023546876</ref><references group="xtra"/><references/>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Bonnet, M.]]		[[Category: Bonnet, M.]]

OCA at 22:45, 10 April 2013

2013-04-10T22:45:31Z

←Older revision		Revision as of 22:45, 10 April 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4i2o\| PDB=4i2o \| SCENE= }}
		+	===The Structure of FixK2 from Bradyrhizobium japonicum===

-	~~The entry~~ 4i2o is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4i2o]] is a 4 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=4I2O OCA].
-	~~Authors~~: Bonnet, M.~~, Kurz, M., Mesa, S.,~~ Briand, C., Gruetter, M.G., Hennecke, H.	+	[[Category: Bradyrhizobium japonicum]]
-		+	[[Category: Bonnet, M.]]
-	~~Description~~: ~~The Structure of FixK2 from Bradyrhizobium japonicum~~	+	[[Category: Briand, C.]]
		+	[[Category: Gruetter, M G.]]
		+	[[Category: Hennecke, H.]]
		+	[[Category: Kurz, M.]]
		+	[[Category: Mesa, S.]]
		+	[[Category: Crp/fnr superfamily]]
		+	[[Category: Transcription regulator-dna complex]]

OCA at 11:02, 19 December 2012

2012-12-19T11:02:54Z

←Older revision		Revision as of 11:02, 19 December 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i2o is ON HOLD	+	The entry 4i2o is ON HOLD until Paper Publication

	Authors: Bonnet, M., Kurz, M., Mesa, S., Briand, C., Gruetter, M.G., Hennecke, H.		Authors: Bonnet, M., Kurz, M., Mesa, S., Briand, C., Gruetter, M.G., Hennecke, H.

	Description: The Structure of FixK2 from Bradyrhizobium japonicum		Description: The Structure of FixK2 from Bradyrhizobium japonicum

OCA: Protected "4i2o" [edit=sysop:move=sysop]

2012-11-28T14:08:35Z

Protected "4i2o" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:08, 28 November 2012

OCA: New page: '''Unreleased structure''' The entry 4i2o is ON HOLD Authors: Bonnet, M., Kurz, M., Mesa, S., Briand, C., Gruetter, M.G., Hennecke, H. Description: The Structure of FixK2 from Bradyrhi...

2012-11-28T14:08:34Z

New page: '''Unreleased structure''' The entry 4i2o is ON HOLD Authors: Bonnet, M., Kurz, M., Mesa, S., Briand, C., Gruetter, M.G., Hennecke, H. Description: The Structure of FixK2 from Bradyrhi...

New page

'''Unreleased structure'''

The entry 4i2o is ON HOLD

Authors: Bonnet, M., Kurz, M., Mesa, S., Briand, C., Gruetter, M.G., Hennecke, H.

Description: The Structure of FixK2 from Bradyrhizobium japonicum