6h9e - Revision history

OCA at 11:51, 1 February 2024

OCA — Thu, 01 Feb 2024 11:51:08 GMT

←Older revision		Revision as of 11:51, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6h9e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_cochlearium Clostridium cochlearium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6H9E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6h9e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_cochlearium Clostridium cochlearium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6H9E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=FWK:(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol'>FWK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</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]] 1.82Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=FWK:(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol'>FWK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</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=6h9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h9e OCA], [https://pdbe.org/6h9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6h9e RCSB], [https://www.ebi.ac.uk/pdbsum/6h9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6h9e 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=6h9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h9e OCA], [https://pdbe.org/6h9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6h9e RCSB], [https://www.ebi.ac.uk/pdbsum/6h9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6h9e ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:20, 26 October 2022

OCA — Wed, 26 Oct 2022 06:20:39 GMT

←Older revision		Revision as of 06:20, 26 October 2022
Line 3:		Line 3:
	<StructureSection load='6h9e' size='340' side='right'caption='[[6h9e]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='6h9e' size='340' side='right'caption='[[6h9e]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6h9e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H9E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6H9E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6h9e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_cochlearium Clostridium cochlearium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6H9E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=FWK:(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol'>FWK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=FWK:(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol'>FWK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylaspartate_mutase Methylaspartate mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.1 5.4.99.1] </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=6h9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h9e OCA], [https://pdbe.org/6h9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6h9e RCSB], [https://www.ebi.ac.uk/pdbsum/6h9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6h9e 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=6h9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h9e OCA], [~~http~~://pdbe.org/6h9e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6h9e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6h9e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6h9e ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GMSS_CLOCO GMSS_CLOCO]] Catalyzes the carbon skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate ((2S,3S)-3-methylaspartate).[HAMAP-Rule:MF_00526]<ref>PMID:1315276</ref> <ref>PMID:7880251</ref> <ref>PMID:8013871</ref> ~~[[http~~:~~//www.uniprot.org/uniprot/GLME_CLOCO GLME_CLOCO]] Catalyzes~~ the ~~carbon skeleton rearrangement~~ of L-glutamate ~~to L~~-~~threo~~-3-~~methylaspartate ((2S~~,~~3S)~~-3-~~methylaspartate~~).<ref>PMID:~~7880251~~</ref> <~~ref~~>~~PMID~~:~~1315276~~</~~ref~~>	+	[https://www.uniprot.org/uniprot/GMSS_CLOCO GMSS_CLOCO] Catalyzes the carbon skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate ((2S,3S)-3-methylaspartate).[HAMAP-Rule:MF_00526]<ref>PMID:1315276</ref> <ref>PMID:7880251</ref> <ref>PMID:8013871</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5'-deoxy-5'adenosyl radical, which originates from reversible Co-C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 10(12) -fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate-loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co-C bond cleavage. Strategically interacting adjacent adenosine- and substrate-binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl-dependent mutases.
		+
		+	Structure-Based Demystification of Radical Catalysis by a Coenzyme B12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues.,Gruber K, Csitkovits V, Lyskowski A, Kratky C, Krautler B Angew Chem Int Ed Engl. 2022 Aug 26;61(35):e202208295. doi:, 10.1002/anie.202208295. Epub 2022 Jul 21. PMID:35793207<ref>PMID:35793207</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6h9e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium cochlearium]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Methylaspartate mutase]]~~	+	[[Category: Csitkovits V]]
-	[[Category: Csitkovits, V]]	+	[[Category: Gruber K]]
-	[[Category: Gruber, K]]	+	[[Category: Kratky C]]
-	[[Category: Kratky, C]]	+
-	~~[[Category: Co-c-bond]]~~	+
-	~~[[Category: Coenzyme b12]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Radical reaction]]~~	+
-	~~[[Category: Rossman-fold]]~~	+
-	~~[[Category: Tim-barrel~~]]	+

OCA at 16:30, 14 August 2019

OCA — Wed, 14 Aug 2019 16:30:10 GMT

←Older revision		Revision as of 16:30, 14 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6h9e is ~~ON HOLD until Paper Publication~~	+	==Structure of glutamate mutase reconstituted with homo-coenzyme B12==
-		+	<StructureSection load='6h9e' size='340' side='right'caption='[[6h9e]], [[Resolution\|resolution]] 1.82Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6h9e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H9E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H9E FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=FWK:(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol'>FWK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylaspartate_mutase Methylaspartate mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.1 5.4.99.1] </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=6h9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h9e OCA], [http://pdbe.org/6h9e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h9e RCSB], [http://www.ebi.ac.uk/pdbsum/6h9e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h9e ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GMSS_CLOCO GMSS_CLOCO]] Catalyzes the carbon skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate ((2S,3S)-3-methylaspartate).[HAMAP-Rule:MF_00526]<ref>PMID:1315276</ref> <ref>PMID:7880251</ref> <ref>PMID:8013871</ref> [[http://www.uniprot.org/uniprot/GLME_CLOCO GLME_CLOCO]] Catalyzes the carbon skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate ((2S,3S)-3-methylaspartate).<ref>PMID:7880251</ref> <ref>PMID:1315276</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Methylaspartate mutase]]
		+	[[Category: Csitkovits, V]]
		+	[[Category: Gruber, K]]
		+	[[Category: Kratky, C]]
		+	[[Category: Co-c-bond]]
		+	[[Category: Coenzyme b12]]
		+	[[Category: Isomerase]]
		+	[[Category: Radical reaction]]
		+	[[Category: Rossman-fold]]
		+	[[Category: Tim-barrel]]

OCA: Protected "6h9e" [edit=sysop:move=sysop]

OCA — Wed, 15 Aug 2018 14:59:46 GMT

Protected "6h9e" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:59, 15 August 2018

OCA: New page: '''Unreleased structure''' The entry 6h9e is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Aug 2018 14:59:45 GMT

New page: '''Unreleased structure''' The entry 6h9e is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6h9e is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]