5dco - Revision history

OCA at 11:25, 10 January 2024

2024-01-10T11:25:42Z

←Older revision		Revision as of 11:25, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DCO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DCO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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]] 2.326Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [https://pdbe.org/5dco PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [https://www.ebi.ac.uk/pdbsum/5dco PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dco 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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [https://pdbe.org/5dco PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [https://www.ebi.ac.uk/pdbsum/5dco PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dco ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:30, 21 June 2023

2023-06-21T10:30:25Z

←Older revision		Revision as of 10:30, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5dco' size='340' side='right'caption='[[5dco]], [[Resolution\|resolution]] 2.33Å' scene=''>		<StructureSection load='5dco' size='340' side='right'caption='[[5dco]], [[Resolution\|resolution]] 2.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geoka Geoka~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DCO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DCO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xbv\|4xbv]], [[4xb9\|4xb9]], [[4xbw\|4xbw]]</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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [https://pdbe.org/5dco PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [https://www.ebi.ac.uk/pdbsum/5dco PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dco ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [~~http~~://pdbe.org/5dco PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dco PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dco ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5KW80_GEOKA Q5KW80_GEOKA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geoka~~]]	+	[[Category: Geobacillus kaustophilus HTA426]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonucleoside-diphosphate reductase]]~~	+	[[Category: Griese JJ]]
-	[[Category: Griese~~, J J~~]]	+	[[Category: Hogbom M]]
-	[[Category: Hogbom, M]]	+
-	~~[[Category: Diiron cofactor]]~~	+
-	~~[[Category: Metalloprotein oxidoreductase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: R2-like ligand-binding oxidase]]~~	+
-	~~[[Category: Ribonucleotide reductase r2 subunit fold~~]]	+

OCA at 07:59, 8 April 2020

2020-04-08T07:59:24Z

←Older revision		Revision as of 07:59, 8 April 2020
Line 1:		Line 1:
		+
	==R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor (short soak)==		==R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor (short soak)==
-	<StructureSection load='5dco' size='340' side='right' caption='[[5dco]], [[Resolution\|resolution]] 2.33Å' scene=''>	+	<StructureSection load='5dco' size='340' side='right'caption='[[5dco]], [[Resolution\|resolution]] 2.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DCO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DCO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xbv\|4xbv]], [[4xb9\|4xb9]], [[4xbw\|4xbw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xbv\|4xbv]], [[4xb9\|4xb9]], [[4xbw\|4xbw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [http://pdbe.org/5dco PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [http://www.ebi.ac.uk/pdbsum/5dco PDBsum]</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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [http://pdbe.org/5dco PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [http://www.ebi.ac.uk/pdbsum/5dco PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dco ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5dco" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dco" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geoka]]
		+	[[Category: Large Structures]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Griese, J J]]		[[Category: Griese, J J]]

OCA at 21:57, 30 November 2015

2015-11-30T21:57:45Z

←Older revision		Revision as of 21:57, 30 November 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xbv\|4xbv]], [[4xb9\|4xb9]], [[4xbw\|4xbw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xbv\|4xbv]], [[4xb9\|4xb9]], [[4xbw\|4xbw]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [http://www.ebi.ac.uk/pdbsum/5dco 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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [http://pdbe.org/5dco PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [http://www.ebi.ac.uk/pdbsum/5dco PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	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 5dco" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:13, 9 September 2015

2015-09-09T11:13:50Z

←Older revision		Revision as of 11:13, 9 September 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor (short soak)==
		+	<StructureSection load='5dco' size='340' side='right' caption='[[5dco]], [[Resolution\|resolution]] 2.33Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dco]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DCO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xbv\|4xbv]], [[4xb9\|4xb9]], [[4xbw\|4xbw]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=5dco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dco OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5dco RCSB], [http://www.ebi.ac.uk/pdbsum/5dco PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two recently discovered groups of prokaryotic di-metal carboxylate proteins harbor a heterodinuclear Mn/Fe cofactor. These are the class Ic ribonucleotide reductase R2 proteins and a group of oxidases that are found predominantly in pathogens and extremophiles, called R2-like ligand-binding oxidases (R2lox). We have recently shown that the Mn/Fe cofactor of R2lox self-assembles from MnII and FeII in vitro and catalyzes formation of a tyrosine-valine ether crosslink in the protein scaffold [Griese JJ et al. (2013) Proc. Natl. Acad. Sci. USA 110:17189-17194]. Here we present a detailed structural analysis of R2lox in the non-activated, reduced and oxidized resting Mn/Fe- and Fe/Fe-bound states, as well as the non-activated Mn/Mn-bound state. X-ray crystallography and X-ray absorption spectroscopy demonstrate that the active site ligand configuration of R2lox is essentially the same regardless of cofactor composition. Both the Mn/Fe and the diiron cofactor activate oxygen and catalyze formation of the ether crosslink, whereas the dimanganese cluster does not. The structures delineate likely routes for gated oxygen and substrate access to the active site that are controlled by the redox state of the cofactor. These results suggest that oxygen activation proceeds via the same mechanism at the Mn/Fe and Fe/Fe center, and that R2lox proteins might utilize either cofactor in vivo based on metal availability.

-	~~The entry 5dco is ON HOLD until Paper Publication~~	+	Structural Basis for Oxygen Activation at a Heterodinuclear Mn/Fe Cofactor.,Griese JJ, Kositzki R, Schrapers P, Branca RM, Nordstrom A, Lehtio J, Haumann M, Hogbom M J Biol Chem. 2015 Aug 31. pii: jbc.M115.675223. PMID:26324712<ref>PMID:26324712</ref>

-	~~Authors: Griese~~, J.J.~~, Hogbom, M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor (short soak)~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: Griese, J.J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribonucleoside-diphosphate reductase]]
		+	[[Category: Griese, J J]]
	[[Category: Hogbom, M]]		[[Category: Hogbom, M]]
		+	[[Category: Diiron cofactor]]
		+	[[Category: Metalloprotein oxidoreductase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: R2-like ligand-binding oxidase]]
		+	[[Category: Ribonucleotide reductase r2 subunit fold]]

OCA: Protected "5dco" [edit=sysop:move=sysop]

2015-09-02T11:28:01Z

Protected "5dco" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:28, 2 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dco is ON HOLD until Paper Publication Authors: Griese, J.J., Hogbom, M. Description: R2-like ligand-binding oxidase with aerobically reconstitute...

2015-09-02T11:27:59Z

New page: '''Unreleased structure''' The entry 5dco is ON HOLD until Paper Publication Authors: Griese, J.J., Hogbom, M. Description: R2-like ligand-binding oxidase with aerobically reconstitute...

New page

'''Unreleased structure'''

The entry 5dco is ON HOLD until Paper Publication

Authors: Griese, J.J., Hogbom, M.

Description: R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor (short soak)
[[Category: Unreleased Structures]]
[[Category: Griese, J.J]]
[[Category: Hogbom, M]]