6i94 - Revision history

OCA at 11:49, 24 January 2024

OCA — Wed, 24 Jan 2024 11:49:42 GMT

←Older revision		Revision as of 11:49, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6i94' size='340' side='right'caption='[[6i94]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6i94' size='340' side='right'caption='[[6i94]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i94]] 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=6I94 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i94]] 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=6I94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I94 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</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]] 1.703Å</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]], [[5omk\|5omk]], [[5omj\|5omj]], [[6f65\|6f65]], [[6f6b\|6f6b]], [[6f6c\|6f6c]], [[6f6e\|6f6e]], [[6f6f\|6f6f]], [[6f6g\|6f6g]], [[6f6h\|6f6h]], [[6f6k\|6f6k]], [[6f6l\|6f6l]], [[6f6m\|6f6m]], [[6i93\|6i93]], [[6i92\|6i92]], [[6i95\|6i95]], [[6i90\|6i90]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</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=6i94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i94 OCA], [https://pdbe.org/6i94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i94 RCSB], [https://www.ebi.ac.uk/pdbsum/6i94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i94 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=6i94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i94 OCA], [~~http~~://pdbe.org/6i94 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i94 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i94 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i94 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 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6i94" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6i94" 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 07:55, 23 October 2019

OCA — Wed, 23 Oct 2019 07:55:03 GMT

←Older revision		Revision as of 07:55, 23 October 2019
Line 3:		Line 3:
	<StructureSection load='6i94' size='340' side='right'caption='[[6i94]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6i94' size='340' side='right'caption='[[6i94]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i94]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i94]] 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=6I94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I94 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</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]], [[5omk\|5omk]], [[5omj\|5omj]], [[6f65\|6f65]], [[6f6b\|6f6b]], [[6f6c\|6f6c]], [[6f6e\|6f6e]], [[6f6f\|6f6f]], [[6f6g\|6f6g]], [[6f6h\|6f6h]], [[6f6k\|6f6k]], [[6f6l\|6f6l]], [[6f6m\|6f6m]], [[6i93\|6i93]], [[6i92\|6i92]], [[6i95\|6i95]], [[6i90\|6i90]]</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]], [[5omk\|5omk]], [[5omj\|5omj]], [[6f65\|6f65]], [[6f6b\|6f6b]], [[6f6c\|6f6c]], [[6f6e\|6f6e]], [[6f6f\|6f6f]], [[6f6g\|6f6g]], [[6f6h\|6f6h]], [[6f6k\|6f6k]], [[6f6l\|6f6l]], [[6f6m\|6f6m]], [[6i93\|6i93]], [[6i92\|6i92]], [[6i95\|6i95]], [[6i90\|6i90]]</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=6i94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i94 OCA], [http://pdbe.org/6i94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i94 RCSB], [http://www.ebi.ac.uk/pdbsum/6i94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i94 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=6i94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i94 OCA], [http://pdbe.org/6i94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i94 RCSB], [http://www.ebi.ac.uk/pdbsum/6i94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i94 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A heterobimetallic Mn/Fe cofactor is present in the R2 subunit of class Ic ribonucleotide reductases (R2c) and in R2-like ligand-binding oxidases (R2lox). Although the protein-derived metal ligands are the same in both groups of proteins, the connectivity of the two metal ions and the chemistry each cofactor performs are different: in R2c, a one-electron oxidant, the Mn/Fe dimer is linked by two oxygen bridges (mu-oxo/mu-hydroxo), whereas in R2lox, a two-electron oxidant, it is linked by a single oxygen bridge (mu-hydroxo) and a fatty acid ligand. Here, we identified a second coordination sphere residue that directs the divergent reactivity of the protein scaffold. We found that the residue that directly precedes the N-terminal carboxylate metal ligand is conserved as a glycine within the R2lox group, but not in R2c. Substitution of the glycine with leucine converted the resting-state R2lox cofactor to an R2c-like cofactor, a micro-oxo/micro-hydroxo-bridged MnIII/FeIII dimer. This species has recently been observed as an intermediate of the oxygen activation reaction in wild-type R2lox, indicating that it is physiologically relevant. Cofactor maturation in R2c and R2lox therefore follows the same pathway, with structural and functional divergence of the two cofactor forms following oxygen activation. We also show that the leucine-substituted variant no longer functions as a two-electron oxidant. Our results reveal that the residue preceding the N-terminal metal ligand directs the cofactor's reactivity toward one- or two-electron redox chemistry, presumably by setting the protonation state of the bridging oxygens and thereby perturbing the redox potential of the Mn ion.
		+
		+	Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins.,Kutin Y, Kositzki R, Branca RMM, Srinivas V, Lundin D, Haumann M, Hogbom M, Cox N, Griese JJ J Biol Chem. 2019 Oct 7. pii: RA119.010570. doi: 10.1074/jbc.RA119.010570. PMID:31591267<ref>PMID:31591267</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6i94" 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 05:49, 16 October 2019

OCA — Wed, 16 Oct 2019 05:49:48 GMT

←Older revision		Revision as of 05:49, 16 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6i94 is ON HOLD until Paper Publication~~	+	==R2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after aerobic reconstitution with Mn and Fe)==
-		+	<StructureSection load='6i94' size='340' side='right'caption='[[6i94]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors: Griese, J.J., Hogbom, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6i94]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I94 FirstGlance]. <br>
-	~~Description:~~ R2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after aerobic reconstitution with Mn and Fe)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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]], [[5omk\|5omk]], [[5omj\|5omj]], [[6f65\|6f65]], [[6f6b\|6f6b]], [[6f6c\|6f6c]], [[6f6e\|6f6e]], [[6f6f\|6f6f]], [[6f6g\|6f6g]], [[6f6h\|6f6h]], [[6f6k\|6f6k]], [[6f6l\|6f6l]], [[6f6m\|6f6m]], [[6i93\|6i93]], [[6i92\|6i92]], [[6i95\|6i95]], [[6i90\|6i90]]</td></tr>
-	[[Category: Griese, J.J]]	+	<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=6i94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i94 OCA], [http://pdbe.org/6i94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i94 RCSB], [http://www.ebi.ac.uk/pdbsum/6i94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i94 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ribonucleoside-diphosphate reductase]]
		+	[[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 04:58, 5 December 2018

OCA — Wed, 05 Dec 2018 04:58:46 GMT

←Older revision		Revision as of 04:58, 5 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i94 is ON HOLD	+	The entry 6i94 is ON HOLD until Paper Publication

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

OCA: Protected "6i94" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 18:46:38 GMT

Protected "6i94" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:46, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6i94 is ON HOLD Authors: Griese, J.J., Hogbom, M. Description: R2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after ...

OCA — Sun, 02 Dec 2018 18:46:36 GMT

New page: '''Unreleased structure''' The entry 6i94 is ON HOLD Authors: Griese, J.J., Hogbom, M. Description: R2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after ...

New page

'''Unreleased structure'''

The entry 6i94 is ON HOLD

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

Description: R2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after aerobic reconstitution with Mn and Fe)
[[Category: Unreleased Structures]]
[[Category: Griese, J.J]]
[[Category: Hogbom, M]]