6qk1 - Revision history

OCA at 12:02, 24 January 2024

OCA — Wed, 24 Jan 2024 12:02:33 GMT

←Older revision		Revision as of 12:02, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6qk1' size='340' side='right'caption='[[6qk1]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6qk1' size='340' side='right'caption='[[6qk1]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qk1]] 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=6QK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6QK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qk1]] 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=6QK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QK1 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</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]] 1.754Å</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='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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6qk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk1 OCA], [https://pdbe.org/6qk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qk1 RCSB], [https://www.ebi.ac.uk/pdbsum/6qk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk1 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=6qk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk1 OCA], [~~http~~://pdbe.org/6qk1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qk1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qk1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk1 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 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6qk1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6qk1" 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: 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: Metalloprotein oxidoreductase]]~~	+
-	~~[[Category: Mn/fe cofactor]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: R2-like ligand-binding oxidase]]~~	+
-	~~[[Category: Ribonucleotide reductase r2 subunit fold~~]]	+

OCA at 11:26, 26 August 2020

OCA — Wed, 26 Aug 2020 11:26:16 GMT

←Older revision		Revision as of 11:26, 26 August 2020
Line 3:		Line 3:
	<StructureSection load='6qk1' size='340' side='right'caption='[[6qk1]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6qk1' size='340' side='right'caption='[[6qk1]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qk1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QK1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qk1]] 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=6QK1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QK1 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></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=6qk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk1 OCA], [http://pdbe.org/6qk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6qk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk1 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=6qk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk1 OCA], [http://pdbe.org/6qk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6qk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater Mn(II) affinity than Fe(II) affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.
		+
		+	Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein.,Kisgeropoulos EC, Griese JJ, Smith ZR, Branca RMM, Schneider CR, Hogbom M, Shafaat HS J Am Chem Soc. 2020 Mar 18;142(11):5338-5354. doi: 10.1021/jacs.0c00333. Epub, 2020 Mar 9. PMID:32062969<ref>PMID:32062969</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6qk1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geoka]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]

OCA at 06:28, 19 February 2020

OCA — Wed, 19 Feb 2020 06:28:15 GMT

←Older revision		Revision as of 06:28, 19 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qk1 ~~is ON HOLD until Paper Publication~~	+	==R2-like ligand-binding oxidase Y175F mutant with aerobically reconstituted Mn/Fe cofactor==
-		+	<StructureSection load='6qk1' size='340' side='right'caption='[[6qk1]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6qk1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QK1 FirstGlance]. <br>
-	~~Description~~:	+	</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6qk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qk1 OCA], [http://pdbe.org/6qk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6qk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qk1 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ribonucleoside-diphosphate reductase]]
		+	[[Category: Griese, J J]]
		+	[[Category: Hogbom, M]]
		+	[[Category: Metalloprotein oxidoreductase]]
		+	[[Category: Mn/fe cofactor]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: R2-like ligand-binding oxidase]]
		+	[[Category: Ribonucleotide reductase r2 subunit fold]]

OCA: Protected "6qk1" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 07:57:55 GMT

Protected "6qk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:57, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qk1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Feb 2019 07:57:54 GMT

New page: '''Unreleased structure''' The entry 6qk1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6qk1 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]