OCA at 16:56, 18 October 2023

OCA — Wed, 18 Oct 2023 16:56:06 GMT

←Older revision		Revision as of 16:56, 18 October 2023
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-	====	+	==Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis==
-	<StructureSection load='7sxm' size='340' side='right'caption='[[7sxm]]' scene=''>	+	<StructureSection load='7sxm' size='340' side='right'caption='[[7sxm]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7sxm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_marburgensis_str._Marburg Methanothermobacter marburgensis str. Marburg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SXM FirstGlance]. <br>
-	</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=7sxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sxm OCA], [https://pdbe.org/7sxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sxm RCSB], [https://www.ebi.ac.uk/pdbsum/7sxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sxm ProSAT]</span></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]] 2.503Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AGM:5-METHYL-ARGININE'>AGM</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=DYA:DIDEHYDROASPARTATE'>DYA</scene>, <scene name='pdbligand=F43:FACTOR+430'>F43</scene>, <scene name='pdbligand=GL3:THIOGLYCIN'>GL3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MGN:2-METHYL-GLUTAMINE'>MGN</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=XE:XENON'>XE</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=7sxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sxm OCA], [https://pdbe.org/7sxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sxm RCSB], [https://www.ebi.ac.uk/pdbsum/7sxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sxm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MCRA_METTM MCRA_METTM] Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and a heterodisulfide.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methyl-Coenzyme M Reductase (MCR) catalyzes the biosynthesis of methane in methanogenic archaea, using a catalytic Ni-centered Cofactor F430 in its active site. It also catalyzes the reverse reaction, that is, the anaerobic activation and oxidation, including the cleavage of the CH bond in methane. Because methanogenesis is the major source of methane on earth, understanding the reaction mechanism of this enzyme can have massive implications in global energy balances. While recent publications have proposed a radical-based catalytic mechanism as well as novel sulfonate-based binding modes of MCR for its native substrates, the structure of the active state of MCR, as well as a complete characterization of the reaction, remain elusive. Previous attempts to structurally characterize the active MCR-Ni(I) state have been unsuccessful due to oxidation of the redox- sensitive catalytic Ni center. Further, while many cryo structures of the inactive Ni(II)-enzyme in various substrates-bound forms have been published, no room temperature structures have been reported, and the structure and mechanism of MCR under physiologically relevant conditions is not known. In this study, we report the first room temperature structure of the MCRred1-silent Ni(II) form using an X-ray Free-Electron Laser (XFEL), with simultaneous X-ray Emission Spectroscopy (XES) and X-ray Diffraction (XRD) data collection. In celebration of the seminal contributions of inorganic chemist Dick Holm to our understanding of nickel-based catalysis, we are honored to announce our findings in this special issue dedicated to this remarkable pioneer of bioinorganic chemistry.
		+
		+	XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase.,Ohmer CJ, Dasgupta M, Patwardhan A, Bogacz I, Kaminsky C, Doyle MD, Chen PY, Keable SM, Makita H, Simon PS, Massad R, Fransson T, Chatterjee R, Bhowmick A, Paley DW, Moriarty NW, Brewster AS, Gee LB, Alonso-Mori R, Moss F, Fuller FD, Batyuk A, Sauter NK, Bergmann U, Drennan CL, Yachandra VK, Yano J, Kern JF, Ragsdale SW J Inorg Biochem. 2022 May;230:111768. doi: 10.1016/j.jinorgbio.2022.111768. Epub , 2022 Feb 17. PMID:35202981<ref>PMID:35202981</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7sxm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Methanothermobacter marburgensis str. Marburg]]
		+	[[Category: Chen PY-T]]
		+	[[Category: Drennan CL]]

OCA at 10:26, 6 April 2022

OCA — Wed, 06 Apr 2022 10:26:09 GMT

←Older revision		Revision as of 10:26, 6 April 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7sxm ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7sxm' size='340' side='right'caption='[[7sxm]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7sxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sxm OCA], [https://pdbe.org/7sxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sxm RCSB], [https://www.ebi.ac.uk/pdbsum/7sxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sxm ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 14:02, 22 December 2021

OCA — Wed, 22 Dec 2021 14:02:37 GMT

←Older revision		Revision as of 14:02, 22 December 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7sxm is ON HOLD	+	The entry 7sxm is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7sxm" [edit=sysop:move=sysop]

OCA — Wed, 01 Dec 2021 05:14:38 GMT

Protected "7sxm" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:14, 1 December 2021

OCA: New page: '''Unreleased structure''' The entry 7sxm is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Dec 2021 05:14:37 GMT

New page: '''Unreleased structure''' The entry 7sxm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7sxm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7sxm - Revision history

OCA at 16:56, 18 October 2023

OCA at 10:26, 6 April 2022

OCA at 14:02, 22 December 2021

OCA: Protected "7sxm" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7sxm is ON HOLD Authors: Description: Category: Unreleased Structures