6cwo - Revision history

OCA at 14:31, 13 March 2024

OCA — Wed, 13 Mar 2024 14:31:06 GMT

←Older revision		Revision as of 14:31, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6cwo' size='340' side='right'caption='[[6cwo]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='6cwo' size='340' side='right'caption='[[6cwo]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6CWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cwo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_johnsoniae_UW101 Flavobacterium johnsoniae UW101]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CWO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.87Å</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=6cwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwo OCA], [~~http~~://pdbe.org/6cwo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cwo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cwo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwo ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6cwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwo OCA], [https://pdbe.org/6cwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cwo RCSB], [https://www.ebi.ac.uk/pdbsum/6cwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwo ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A5FCJ5_FLAJ1 A5FCJ5_FLAJ1]
-	A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its beta subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2(-)) for activation, but it does not require the O2(-)-supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj beta has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj beta directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) betas. This tendency makes Fj beta unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2(-) to the Mn2(II/II) cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj beta is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-beta.	+
-		+
-	Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor.,Rose HR, Ghosh MK, Maggiolo AO, Pollock CJ, Blaesi EJ, Hajj V, Wei Y, Rajakovich LJ, Chang WC, Han Y, Hajj M, Krebs C, Silakov A, Pandelia ME, Bollinger JM Jr., Boal AK Biochemistry. 2018 Apr 17. doi: ~~10.1021~~/~~acs.biochem.8b00247. PMID:29609464<ref>PMID:29609464<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6cwo" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]		*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium johnsoniae UW101]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boal~~, A K~~]]	+	[[Category: Boal AK]]
-	[[Category: Maggiolo~~, A O~~]]	+	[[Category: Maggiolo AO]]
-	[[Category: Rose~~, H R]]~~	+	[[Category: Rose HR]]
-	~~[[Category: Dimanganese cluster]]~~	+
-	~~[[Category: Four-helix bundle]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxidoretuctase]]~~	+
-	~~[[Category: Ribonucleotide reductase~~]]	+

OCA at 09:01, 11 November 2020

OCA — Wed, 11 Nov 2020 09:01:41 GMT

←Older revision		Revision as of 09:01, 11 November 2020
Line 1:		Line 1:

	==X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (aerobic)==		==X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (aerobic)==
-	<StructureSection load='6cwo' size='340' side='right' caption='[[6cwo]], [[Resolution\|resolution]] 1.87Å' scene=''>	+	<StructureSection load='6cwo' size='340' side='right'caption='[[6cwo]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6CWO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=6cwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwo OCA], [http://pdbe.org/6cwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cwo RCSB], [http://www.ebi.ac.uk/pdbsum/6cwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwo 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=6cwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwo OCA], [http://pdbe.org/6cwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cwo RCSB], [http://www.ebi.ac.uk/pdbsum/6cwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 6cwo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cwo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Boal, A K]]		[[Category: Boal, A K]]
	[[Category: Maggiolo, A O]]		[[Category: Maggiolo, A O]]

OCA at 05:37, 27 June 2018

OCA — Wed, 27 Jun 2018 05:37:11 GMT

←Older revision		Revision as of 05:37, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cwo is ~~ON HOLD until Paper~~ Publication	+	==X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (aerobic)==
		+	<StructureSection load='6cwo' size='340' side='right' caption='[[6cwo]], [[Resolution\|resolution]] 1.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CWO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=6cwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwo OCA], [http://pdbe.org/6cwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cwo RCSB], [http://www.ebi.ac.uk/pdbsum/6cwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwo ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its beta subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2(-)) for activation, but it does not require the O2(-)-supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj beta has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj beta directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) betas. This tendency makes Fj beta unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2(-) to the Mn2(II/II) cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj beta is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-beta.

-	~~Authors:~~ Maggiolo, A~~.O.~~, ~~Rose~~, ~~H.R~~., Boal~~, A~~.K.	+	Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor.,Rose HR, Ghosh MK, Maggiolo AO, Pollock CJ, Blaesi EJ, Hajj V, Wei Y, Rajakovich LJ, Chang WC, Han Y, Hajj M, Krebs C, Silakov A, Pandelia ME, Bollinger JM Jr., Boal AK Biochemistry. 2018 Apr 17. doi: 10.1021/acs.biochem.8b00247. PMID:29609464<ref>PMID:29609464</ref>

-	~~Description: X-ray crystal structure~~ of ~~Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (aerobic)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Maggiolo, A.O]]	+	<div class="pdbe-citations 6cwo" style="background-color:#fffaf0;"></div>
-	[[Category: Rose, H.R]]	+	== References ==
-	[[Category: ~~Boal, A.K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boal, A K]]
		+	[[Category: Maggiolo, A O]]
		+	[[Category: Rose, H R]]
		+	[[Category: Dimanganese cluster]]
		+	[[Category: Four-helix bundle]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxidoretuctase]]
		+	[[Category: Ribonucleotide reductase]]

OCA at 04:02, 25 April 2018

OCA — Wed, 25 Apr 2018 04:02:59 GMT

←Older revision		Revision as of 04:02, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Maggiolo, A.O., Rose, H.R., Boal, A.K.		Authors: Maggiolo, A.O., Rose, H.R., Boal, A.K.

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

OCA — Wed, 11 Apr 2018 12:29:38 GMT

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

←Older revision

Revision as of 12:29, 11 April 2018

OCA: New page: '''Unreleased structure''' The entry 6cwo is ON HOLD Authors: Maggiolo, A.O., Rose, H.R., Boal, A.K. Description: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) r...

OCA — Wed, 11 Apr 2018 12:29:37 GMT

New page: '''Unreleased structure''' The entry 6cwo is ON HOLD Authors: Maggiolo, A.O., Rose, H.R., Boal, A.K. Description: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) r...

New page

'''Unreleased structure'''

The entry 6cwo is ON HOLD

Authors: Maggiolo, A.O., Rose, H.R., Boal, A.K.

Description: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (aerobic)
[[Category: Unreleased Structures]]
[[Category: Maggiolo, A.O]]
[[Category: Rose, H.R]]
[[Category: Boal, A.K]]