6bxm - Revision history

OCA at 14:52, 4 October 2023

OCA — Wed, 04 Oct 2023 14:52:20 GMT

←Older revision		Revision as of 14:52, 4 October 2023
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	<StructureSection load='6bxm' size='340' side='right'caption='[[6bxm]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6bxm' size='340' side='right'caption='[[6bxm]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Methanoperedens_nitroreducens Candidatus Methanoperedens nitroreducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.252Å</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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [~~http~~://pdbe.org/6bxm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [https://pdbe.org/6bxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [https://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A062UZ78_9EURY A0A062UZ78_9EURY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candidatus Methanoperedens nitroreducens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carantoa~~, J D~~]]	+	[[Category: Carantoa JD]]
-	[[Category: Dong, M]]	+	[[Category: Dong M]]
-	[[Category: Dzikovski, B]]	+	[[Category: Dzikovski B]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: Ealick SE]]
-	[[Category: Fenwick~~, M K~~]]	+	[[Category: Fenwick MK]]
-	[[Category: Freed~~, J H~~]]	+	[[Category: Freed JH]]
-	[[Category: Hoffman~~, B M~~]]	+	[[Category: Hoffman BM]]
-	[[Category: Kathiresan, V]]	+	[[Category: Kathiresan V]]
-	[[Category: Lancaster~~, K M~~]]	+	[[Category: Lancaster KM]]
-	[[Category: Lin, H]]	+	[[Category: Lin H]]
-	[[Category: Torelli~~, A T~~]]	+	[[Category: Torelli AT]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Diphthamide biosynthesis]]~~	+
-	~~[[Category: Radical sam enzyme~~]]	+

OCA at 08:52, 11 November 2020

OCA — Wed, 11 Nov 2020 08:52:35 GMT

←Older revision		Revision as of 08:52, 11 November 2020
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	==Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM==		==Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM==
-	<StructureSection load='6bxm' size='340' side='right' caption='[[6bxm]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='6bxm' size='340' side='right'caption='[[6bxm]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [http://pdbe.org/6bxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [http://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm 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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [http://pdbe.org/6bxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [http://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Carantoa, J D]]		[[Category: Carantoa, J D]]
	[[Category: Dong, M]]		[[Category: Dong, M]]

OCA at 13:51, 11 April 2018

OCA — Wed, 11 Apr 2018 13:51:19 GMT

←Older revision		Revision as of 13:51, 11 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bxm is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM==
		+	<StructureSection load='6bxm' size='340' side='right' caption='[[6bxm]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BXM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [http://pdbe.org/6bxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [http://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.

-	~~Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y~~., Dong, M., Kathiresan, V., ~~Carantoa~~, ~~J.D.~~, ~~Dzikovski~~, B., Lancaster~~, K.M.~~, Freed, ~~J.H.~~, Hoffman~~, B.M.~~, Lin, H.~~, Ealick, S~~.E.	+	Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.,Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H Science. 2018 Mar 16;359(6381):1247-1250. doi: 10.1126/science.aao6595. PMID:29590073<ref>PMID:29590073</ref>

-	~~Description: Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM~~/~~cleaved SAM~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Ealick~~, S.~~E]]~~	+	<div class="pdbe-citations 6bxm" style="background-color:#fffaf0;"></div>
-	~~[[Category~~: ~~Lancaster, K.M]]~~	+	== References ==
-	[[Category: Carantoa, J.D]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carantoa, J D]]
	[[Category: Dong, M]]		[[Category: Dong, M]]
-	[[Category: Zhang, Y]]
-	[[Category: Freed, J.H]]
	[[Category: Dzikovski, B]]		[[Category: Dzikovski, B]]
-	[[Category: ~~Lin~~, H]]	+	[[Category: Ealick, S E]]
-	[[Category: Hoffman, B.M]]	+	[[Category: Fenwick, M K]]
		+	[[Category: Freed, J H]]
		+	[[Category: Hoffman, B M]]
	[[Category: Kathiresan, V]]		[[Category: Kathiresan, V]]
-	[[Category: ~~Fenwick~~, M.K]]	+	[[Category: Lancaster, K M]]
-	[[Category: Torelli, A.T]]	+	[[Category: Lin, H]]
		+	[[Category: Torelli, A T]]
		+	[[Category: Zhang, Y]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Diphthamide biosynthesis]]
		+	[[Category: Radical sam enzyme]]

OCA at 04:57, 28 February 2018

OCA — Wed, 28 Feb 2018 04:57:35 GMT

←Older revision		Revision as of 04:57, 28 February 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.		Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ealick, S.E]]		[[Category: Ealick, S.E]]
		+	[[Category: Lancaster, K.M]]
	[[Category: Carantoa, J.D]]		[[Category: Carantoa, J.D]]
	[[Category: Dong, M]]		[[Category: Dong, M]]
-	[[Category: Freed, J.H]]
-	[[Category: Lin, H]]
-	[[Category: Torelli, A.T]]
-	[[Category: Lancaster, K.M]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
		+	[[Category: Freed, J.H]]
	[[Category: Dzikovski, B]]		[[Category: Dzikovski, B]]
		+	[[Category: Lin, H]]
	[[Category: Hoffman, B.M]]		[[Category: Hoffman, B.M]]
	[[Category: Kathiresan, V]]		[[Category: Kathiresan, V]]
	[[Category: Fenwick, M.K]]		[[Category: Fenwick, M.K]]
		+	[[Category: Torelli, A.T]]

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

OCA — Wed, 27 Dec 2017 07:21:38 GMT

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

←Older revision

Revision as of 07:21, 27 December 2017

OCA: New page: '''Unreleased structure''' The entry 6bxm is ON HOLD Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J...

OCA — Wed, 27 Dec 2017 07:21:37 GMT

New page: '''Unreleased structure''' The entry 6bxm is ON HOLD Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J...

New page

'''Unreleased structure'''

The entry 6bxm is ON HOLD

Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

Description: Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM
[[Category: Unreleased Structures]]
[[Category: Ealick, S.E]]
[[Category: Carantoa, J.D]]
[[Category: Dong, M]]
[[Category: Freed, J.H]]
[[Category: Lin, H]]
[[Category: Torelli, A.T]]
[[Category: Lancaster, K.M]]
[[Category: Zhang, Y]]
[[Category: Dzikovski, B]]
[[Category: Hoffman, B.M]]
[[Category: Kathiresan, V]]
[[Category: Fenwick, M.K]]