7xrk - Revision history

OCA at 17:59, 29 November 2023

OCA — Wed, 29 Nov 2023 17:59:34 GMT

←Older revision		Revision as of 17:59, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7xrk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XRK FirstGlance]. <br>		<table><tr><td colspan='2'>[[7xrk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XRK 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=CA:CALCIUM+ION'>CA</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=K:POTASSIUM+ION'>K</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]] 2.3Å</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=CA:CALCIUM+ION'>CA</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=K:POTASSIUM+ION'>K</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=7xrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xrk OCA], [https://pdbe.org/7xrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xrk RCSB], [https://www.ebi.ac.uk/pdbsum/7xrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xrk 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=7xrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xrk OCA], [https://pdbe.org/7xrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xrk RCSB], [https://www.ebi.ac.uk/pdbsum/7xrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xrk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:42, 29 March 2023

OCA — Wed, 29 Mar 2023 06:42:38 GMT

←Older revision		Revision as of 06:42, 29 March 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7xrk is ~~ON HOLD until Paper~~ Publication	+	==Diol dehydratase complexed with AdoMeCbl==
		+	<StructureSection load='7xrk' size='340' side='right'caption='[[7xrk]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7xrk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XRK 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=CA:CALCIUM+ION'>CA</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=K:POTASSIUM+ION'>K</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=7xrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xrk OCA], [https://pdbe.org/7xrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xrk RCSB], [https://www.ebi.ac.uk/pdbsum/7xrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xrk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The X-ray structures of coenzyme B(12) (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH(2) group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.

-	~~Authors: Shibata~~, N., ~~Toraya~~, T.	+	Structural Insights into the Very Low Activity of the Homocoenzyme B(12) Adenosylmethylcobalamin in Coenzyme B(12) -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.,Shibata N, Higuchi Y, Krautler B, Toraya T Chemistry. 2022 Nov 21;28(65):e202202196. doi: 10.1002/chem.202202196. Epub 2022 , Sep 19. PMID:35974426<ref>PMID:35974426</ref>

-	~~Description~~: ~~Diol dehydratase complexed with AdoMeCbl~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Shibata, N]]	+	<div class="pdbe-citations 7xrk" style="background-color:#fffaf0;"></div>
-	[[Category: Toraya, T]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Klebsiella oxytoca]]
		+	[[Category: Large Structures]]
		+	[[Category: Shibata N]]
		+	[[Category: Toraya T]]

OCA at 07:42, 24 November 2022

OCA — Thu, 24 Nov 2022 07:42:06 GMT

←Older revision		Revision as of 07:42, 24 November 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Shibata, N., Toraya, T.		Authors: Shibata, N., Toraya, T.

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

OCA — Wed, 18 May 2022 09:12:55 GMT

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

←Older revision

Revision as of 09:12, 18 May 2022

OCA: New page: '''Unreleased structure''' The entry 7xrk is ON HOLD Authors: Shibata, N., Toraya, T. Description: Diol dehydratase complexed with AdoMeCbl Category: Unreleased Structures [[Catego...

OCA — Wed, 18 May 2022 09:12:54 GMT

New page: '''Unreleased structure''' The entry 7xrk is ON HOLD Authors: Shibata, N., Toraya, T. Description: Diol dehydratase complexed with AdoMeCbl Category: Unreleased Structures [[Catego...

New page

'''Unreleased structure'''

The entry 7xrk is ON HOLD

Authors: Shibata, N., Toraya, T.

Description: Diol dehydratase complexed with AdoMeCbl
[[Category: Unreleased Structures]]
[[Category: Shibata, N]]
[[Category: Toraya, T]]