4k8f - Revision history

OCA at 15:55, 20 September 2023

OCA — Wed, 20 Sep 2023 15:55:07 GMT

←Older revision		Revision as of 15:55, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum_ATCC_11170 Rhodospirillum rubrum ATCC 11170]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum_ATCC_11170 Rhodospirillum rubrum ATCC 11170]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K8F 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]] 2.7Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [https://pdbe.org/4k8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [https://www.ebi.ac.uk/pdbsum/4k8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k8f 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=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [https://pdbe.org/4k8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [https://www.ebi.ac.uk/pdbsum/4k8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k8f ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:45, 30 November 2022

OCA — Wed, 30 Nov 2022 11:45:07 GMT

←Older revision		Revision as of 11:45, 30 November 2022
Line 1:		Line 1:

	==Structure of the heme domain of CooA from Rhodospirillum rubrum==		==Structure of the heme domain of CooA from Rhodospirillum rubrum==
-	<StructureSection load='4k8f' size='340' side='right' caption='[[4k8f]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4k8f' size='340' side='right'caption='[[4k8f]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhort Rhort~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4K8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum_ATCC_11170 Rhodospirillum rubrum ATCC 11170]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K8F 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">[[1ft9\|1ft9]]</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=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [https://pdbe.org/4k8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [https://www.ebi.ac.uk/pdbsum/4k8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k8f ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rru_A1431 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269796 RHORT])~~</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=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [~~http~~://pdbe.org/4k8f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4k8f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4k8f ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2RUG3_RHORT Q2RUG3_RHORT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhort~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kuchinskas, M~~]]	+	[[Category: Rhodospirillum rubrum ATCC 11170]]
-	[[Category: ~~Li, H~~]]	+	[[Category: Kuchinskas M]]
-	[[Category: ~~Poulos, T L~~]]	+	[[Category: Li H]]
-	[[Category: ~~Cooa transcription factor]]~~	+	[[Category: Poulos TL]]
-	~~[[Category: Heme protein]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 21:21, 11 August 2016

OCA — Thu, 11 Aug 2016 21:21:37 GMT

←Older revision		Revision as of 21:21, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of the heme domain of CooA from Rhodospirillum rubrum==		==Structure of the heme domain of CooA from Rhodospirillum rubrum==
	<StructureSection load='4k8f' size='340' side='right' caption='[[4k8f]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4k8f' size='340' side='right' caption='[[4k8f]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodospirillum_rubrum_atcc_11170 Rhodospirillum rubrum atcc 11170~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhort Rhort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K8F 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">[[1ft9\|1ft9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ft9\|1ft9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rru_A1431 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269796 ~~Rhodospirillum rubrum ATCC 11170~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rru_A1431 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269796 RHORT])</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=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [http://www.ebi.ac.uk/pdbsum/4k8f 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=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [http://pdbe.org/4k8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [http://www.ebi.ac.uk/pdbsum/4k8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k8f ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4k8f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhodospirillum rubrum atcc 11170~~]]	+	[[Category: Rhort]]
	[[Category: Kuchinskas, M]]		[[Category: Kuchinskas, M]]
	[[Category: Li, H]]		[[Category: Li, H]]

OCA at 14:29, 4 January 2015

OCA — Sun, 04 Jan 2015 14:29:53 GMT

←Older revision		Revision as of 14:29, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4k8f\| PDB=4k8f \| SCENE= }}~~	+	==Structure of the heme domain of CooA from Rhodospirillum rubrum==
-	===Structure of the heme domain of CooA from Rhodospirillum rubrum===	+	<StructureSection load='4k8f' size='340' side='right' caption='[[4k8f]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_16752905}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4k8f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum_atcc_11170 Rhodospirillum rubrum atcc 11170]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K8F 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ft9\|1ft9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rru_A1431 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269796 Rhodospirillum rubrum ATCC 11170])</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=4k8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k8f RCSB], [http://www.ebi.ac.uk/pdbsum/4k8f PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbon monoxide oxidation activator protein (CooA) is a dimeric carbon monoxide (CO) binding transcription factor that in the presence of CO promotes the transcription of genes involved in CO oxidation in Rhodospirillum rubrum. The off state (inactive) of Fe(II) CooA has His and Pro as the two axial heme ligands. In contrast, in the on state, which is active in DNA binding, the Pro ligand bond has been replaced by CO. This occurs by the transient loss of the Pro ligand, thus generating a pentacoordinate heme that can bind CO. The active on state of CooA has two major structural differences from the off state, in addition to the displacement of the Pro ligand by CO. There is a repositioning of long C helices at the dimer interface and a concomitant reorientation of the hinge region between the DNA- and effector-binding domains within each monomer [Roberts et al. (2005) J. Inorg. Biochem. 99, 280-292]. To better understand the relationship of these conformational changes, we have removed the DNA-binding domains and compared CO binding to the truncated and full-length protein. The crystal structure of truncated Fe(II) CooA is the same as that of the effector-binding domain of full-length Fe(II) CooA, including the relative orientation of the homodimer and the ligation environment of the heme. Thus, removing the DNA-binding domains has little obvious effect on the structure of CooA in the inactive off state. However, CO binds about 2-fold more tightly and about 10 times more rapidly to truncated CooA. The rate of CO binding is known to be limited by the dissociation of the Pro heme ligand [Puranik et al. (2004) J. Biol. Chem. 279, 21096-21108]. Therefore, the absence of the DNA-binding domain makes it easier for the Pro ligand to dissociate from the heme iron, which also makes it easier for truncated CooA to adopt the on-state structure.

-	~~==About this Structure==~~	+	The role of the DNA-binding domains in CooA activation.,Kuchinskas M, Li H, Conrad M, Roberts G, Poulos TL Biochemistry. 2006 Jun 13;45(23):7148-53. PMID:16752905<ref>PMID:16752905</ref>
-	~~[[4k8f]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodospirillum_rubrum_atcc_11170 Rhodospirillum rubrum atcc 11170]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:016752905</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Rhodospirillum rubrum atcc 11170]]		[[Category: Rhodospirillum rubrum atcc 11170]]
-	[[Category: Kuchinskas, M.]]	+	[[Category: Kuchinskas, M]]
-	[[Category: Li, H.]]	+	[[Category: Li, H]]
-	[[Category: Poulos, T L.]]	+	[[Category: Poulos, T L]]
	[[Category: Cooa transcription factor]]		[[Category: Cooa transcription factor]]
	[[Category: Heme protein]]		[[Category: Heme protein]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 16:09, 19 June 2013

OCA — Wed, 19 Jun 2013 16:09:30 GMT

←Older revision		Revision as of 16:09, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4k8f\| PDB=4k8f \| SCENE= }}
		+	===Structure of the heme domain of CooA from Rhodospirillum rubrum===
		+	{{ABSTRACT_PUBMED_16752905}}

-	~~The entry~~ 4k8f is ~~ON HOLD~~	+	==About this Structure==
		+	[[4k8f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum_atcc_11170 Rhodospirillum rubrum atcc 11170]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K8F OCA].

-	~~Authors~~: Kuchinskas, M., Li, H., Poulos, T.L.	+	==Reference==
-		+	<ref group="xtra">PMID:016752905</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structure of the heme domain of CooA from Rhodospirillum rubrum~~	+	[[Category: Rhodospirillum rubrum atcc 11170]]
		+	[[Category: Kuchinskas, M.]]
		+	[[Category: Li, H.]]
		+	[[Category: Poulos, T L.]]
		+	[[Category: Cooa transcription factor]]
		+	[[Category: Heme protein]]
		+	[[Category: Transcription]]

OCA: Protected "4k8f" [edit=sysop:move=sysop]

OCA — Wed, 24 Apr 2013 11:02:53 GMT

Protected "4k8f" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:02, 24 April 2013

OCA: New page: '''Unreleased structure''' The entry 4k8f is ON HOLD Authors: Kuchinskas, M., Li, H., Poulos, T.L. Description: Structure of the heme domain of CooA from Rhodospirillum rubrum

OCA — Wed, 24 Apr 2013 11:02:52 GMT

New page: '''Unreleased structure''' The entry 4k8f is ON HOLD Authors: Kuchinskas, M., Li, H., Poulos, T.L. Description: Structure of the heme domain of CooA from Rhodospirillum rubrum

New page

'''Unreleased structure'''

The entry 4k8f is ON HOLD

Authors: Kuchinskas, M., Li, H., Poulos, T.L.

Description: Structure of the heme domain of CooA from Rhodospirillum rubrum