6m2h - Revision history

OCA at 15:12, 29 November 2023

OCA — Wed, 29 Nov 2023 15:12:07 GMT

←Older revision		Revision as of 15:12, 29 November 2023
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	<StructureSection load='6m2h' size='340' side='right'caption='[[6m2h]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6m2h' size='340' side='right'caption='[[6m2h]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metja Metja~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SHN:3,3,3,3-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic+acid'>SHN</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]] 3.1Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbiX, cfbA, MJ0970 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SHN:3,3,3,3-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic+acid'>SHN</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=6m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2h OCA], [https://pdbe.org/6m2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m2h RCSB], [https://www.ebi.ac.uk/pdbsum/6m2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2h ProSAT]</span></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=6m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2h OCA], [https://pdbe.org/6m2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m2h RCSB], [https://www.ebi.ac.uk/pdbsum/6m2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CFBA_METJA CFBA_METJA]] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis. Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation. Catalyzes the insertion of Ni(2+) into sirohydrochlorin to yield Ni-sirohydrochlorin.	+	[https://www.uniprot.org/uniprot/CFBA_METJA CFBA_METJA] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis. Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation. Catalyzes the insertion of Ni(2+) into sirohydrochlorin to yield Ni-sirohydrochlorin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metja~~]]	+	[[Category: Methanocaldococcus jannaschii DSM 2661]]
-	[[Category: Fujishiro, T]]	+	[[Category: Fujishiro T]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Chelatase~~]]	+

OCA at 10:06, 7 July 2021

OCA — Wed, 07 Jul 2021 10:06:34 GMT

←Older revision		Revision as of 10:06, 7 July 2021
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	==A reaction intermediate of sirohydrochlorin nickelochelatase CfbA in complex with Ni2+ and sirohydrochlorin==		==A reaction intermediate of sirohydrochlorin nickelochelatase CfbA in complex with Ni2+ and sirohydrochlorin==
-	<StructureSection load='6m2h' size='340' side='right'caption='[[6m2h]]' scene=''>	+	<StructureSection load='6m2h' size='340' side='right'caption='[[6m2h]], [[Resolution\|resolution]] 3.10Å' 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=6M2H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M2H FirstGlance]. <br>
-	</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=6m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2h OCA], [~~http~~://pdbe.org/6m2h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m2h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m2h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2h ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SHN:3,3,3,3-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic+acid'>SHN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbiX, cfbA, MJ0970 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=6m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2h OCA], [https://pdbe.org/6m2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m2h RCSB], [https://www.ebi.ac.uk/pdbsum/6m2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2h ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CFBA_METJA CFBA_METJA]] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis. Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation. Catalyzes the insertion of Ni(2+) into sirohydrochlorin to yield Ni-sirohydrochlorin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The class II chelatase CfbA catalyzes Ni(2+) insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni(2+) and Co(2+) remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni(2+), Ni-SHC, and Co(2+) were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni(2+)-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co(2+) than Ni(2+). Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni(2+) and Co(2+) by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni(2+) insertion catalytic mechanism was proposed: Ni(2+) insertion to SHC is promoted by the support of an acetate side chain of SHC.
		+
		+	The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis.,Fujishiro T, Ogawa S Chem Sci. 2021 Jan 4;12(6):2172-2180. doi: 10.1039/d0sc05439a. PMID:34163982<ref>PMID:34163982</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6m2h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fujishiro T]]	+	[[Category: Metja]]
		+	[[Category: Fujishiro, T]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Chelatase]]

OCA at 05:47, 20 January 2021

OCA — Wed, 20 Jan 2021 05:47:15 GMT

←Older revision		Revision as of 05:47, 20 January 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6m2h ~~is ON HOLD until Paper Publication~~	+	==A reaction intermediate of sirohydrochlorin nickelochelatase CfbA in complex with Ni2+ and sirohydrochlorin==
-		+	<StructureSection load='6m2h' size='340' side='right'caption='[[6m2h]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M2H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M2H FirstGlance]. <br>
-	~~Description~~:	+	</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=6m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m2h OCA], [http://pdbe.org/6m2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m2h RCSB], [http://www.ebi.ac.uk/pdbsum/6m2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m2h ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fujishiro T]]

OCA at 08:16, 18 March 2020

OCA — Wed, 18 Mar 2020 08:16:35 GMT

←Older revision		Revision as of 08:16, 18 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6m2h is ON HOLD	+	The entry 6m2h is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6m2h" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2020 05:32:07 GMT

Protected "6m2h" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6m2h is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Mar 2020 05:32:06 GMT

New page: '''Unreleased structure''' The entry 6m2h is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6m2h is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]