5omk - Revision history

OCA at 16:54, 13 December 2023

2023-12-13T16:54:45Z

←Older revision		Revision as of 16:54, 13 December 2023
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	==R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before photoconversion==		==R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before photoconversion==
-	<StructureSection load='5omk' size='340' side='right' caption='[[5omk]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5omk' size='340' side='right'caption='[[5omk]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5omk]] 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=5OMK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OMK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5omk]] 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=5OMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OMK 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.704Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]]~~, [[~~4hr4~~\|~~4hr4]], [[4hr5\|4hr5]], [[4xb9\|4xb9]], [[4xbv\|4xbv]], [[4xbw\|4xbw]], [[5dco\|5dco]], [[5dcr\|5dcr]], [[5dcs\|5dcs]], [[5ekb\|5ekb]], [[5omj\|5omj~~]]</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='~~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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omk OCA], [https://pdbe.org/5omk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5omk RCSB], [https://www.ebi.ac.uk/pdbsum/5omk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5omk ProSAT]</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=5omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omk OCA], [~~http~~://pdbe.org/5omk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5omk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5omk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5omk 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 ==
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	</div>		</div>
	<div class="pdbe-citations 5omk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5omk" 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: ~~Ribonucleoside-diphosphate reductase~~]]	+	[[Category: Large Structures]]
-	[[Category: Griese~~, J J~~]]	+	[[Category: Griese JJ]]
-	[[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 07:02, 31 January 2018

2018-01-31T07:02:03Z

←Older revision		Revision as of 07:02, 31 January 2018
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	<StructureSection load='5omk' size='340' side='right' caption='[[5omk]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5omk' size='340' side='right' caption='[[5omk]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5omk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5omk]] 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=5OMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMK 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"><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]], [[4xb9\|4xb9]], [[4xbv\|4xbv]], [[4xbw\|4xbw]], [[5dco\|5dco]], [[5dcr\|5dcr]], [[5dcs\|5dcs]], [[5ekb\|5ekb]], [[5omj\|5omj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hr0\|4hr0]], [[4hr4\|4hr4]], [[4hr5\|4hr5]], [[4xb9\|4xb9]], [[4xbv\|4xbv]], [[4xbw\|4xbw]], [[5dco\|5dco]], [[5dcr\|5dcr]], [[5dcs\|5dcs]], [[5ekb\|5ekb]], [[5omj\|5omj]]</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=5omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omk OCA], [http://pdbe.org/5omk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omk RCSB], [http://www.ebi.ac.uk/pdbsum/5omk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omk 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=5omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omk OCA], [http://pdbe.org/5omk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omk RCSB], [http://www.ebi.ac.uk/pdbsum/5omk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omk ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geoka]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Griese, J J]]		[[Category: Griese, J J]]

OCA at 05:45, 3 January 2018

2018-01-03T05:45:37Z

←Older revision		Revision as of 05:45, 3 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5omk is ~~ON HOLD until Paper~~ Publication	+	==R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before photoconversion==
		+	<StructureSection load='5omk' size='340' side='right' caption='[[5omk]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5omk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMK 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]], [[4xb9\|4xb9]], [[4xbv\|4xbv]], [[4xbw\|4xbw]], [[5dco\|5dco]], [[5dcr\|5dcr]], [[5dcs\|5dcs]], [[5ekb\|5ekb]], [[5omj\|5omj]]</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=5omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omk OCA], [http://pdbe.org/5omk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omk RCSB], [http://www.ebi.ac.uk/pdbsum/5omk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The heterobimetallic R2lox protein binds both manganese and iron ions in a site-selective fashion and activates oxygen, ultimately performing C-H bond oxidation to generate a tyrosine-valine crosslink near the active site. In this work, we demonstrate that following assembly, R2lox undergoes photoinduced changes to the active site geometry and metal coordination motif. Through spectroscopic, structural, and mass spectrometric characterization, the photoconverted species is found to consist of a tyrosinate-bound iron center following light-induced decarboxylation of a coordinating glutamate residue and cleavage of the tyrosine-valine crosslink. This process occurs with high quantum efficiencies (phi= 3%) using violet and near-ultraviolet light, suggesting that the photodecarboxylation is initiated via ligand-to-metal charge transfer excitation. Site-directed mutagenesis and structural analysis suggest that the crosslinked tyrosine-162 is the coordinating residue. One primary product is observed following irradiation, indicating potential use of this class of proteins, which contains a putative substrate channel, for controlled photoinduced decarboxylation processes, with relevance for in vivo functionality of R2lox as well as application in environmental remediation.

-	~~Authors~~:	+	Driving protein conformational changes with light: Photoinduced structural rearrangement in a heterobimetallic oxidase.,Maugeri PT, Griese JJ, Branca RM, Miller EK, Smith ZR, Eirich J, Hogbom M, Shafaat HS J Am Chem Soc. 2017 Dec 22. doi: 10.1021/jacs.7b11966. PMID:29268610<ref>PMID:29268610</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5omk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribonucleoside-diphosphate reductase]]
		+	[[Category: Griese, J J]]
		+	[[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 "5omk" [edit=sysop:move=sysop]

2017-09-27T12:35:43Z

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

←Older revision

Revision as of 12:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5omk is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T12:35:42Z

New page: '''Unreleased structure''' The entry 5omk is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5omk is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]