5yrt - Revision history

OCA at 08:36, 22 November 2023

OCA — Wed, 22 Nov 2023 08:36:14 GMT

←Older revision		Revision as of 08:36, 22 November 2023
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	<StructureSection load='5yrt' size='340' side='right'caption='[[5yrt]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5yrt' size='340' side='right'caption='[[5yrt]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrt]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YRT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrt]] is a 12 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=5YRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YRT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.7Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5yrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrt OCA], [~~http~~://pdbe.org/5yrt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yrt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yrt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrt 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=5yrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrt OCA], [https://pdbe.org/5yrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yrt RCSB], [https://www.ebi.ac.uk/pdbsum/5yrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrt ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q59470_KLEOX Q59470_KLEOX]
	<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: Klebsiella oxytoca]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Propanediol dehydratase]]~~	+	[[Category: Shibata N]]
-	[[Category: Shibata, N]]	+
-	~~[[Category: Adenosylcobalamin]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Radical enzyme~~]]	+

OCA at 09:26, 21 October 2020

OCA — Wed, 21 Oct 2020 09:26:31 GMT

←Older revision		Revision as of 09:26, 21 October 2020
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	==Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal==		==Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal==
-	<StructureSection load='5yrt' size='340' side='right' caption='[[5yrt]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5yrt' size='340' side='right'caption='[[5yrt]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrt]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YRT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrt]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YRT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] </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=5yrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrt OCA], [http://pdbe.org/5yrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrt RCSB], [http://www.ebi.ac.uk/pdbsum/5yrt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrt 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=5yrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrt OCA], [http://pdbe.org/5yrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrt RCSB], [http://www.ebi.ac.uk/pdbsum/5yrt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrt 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: Propanediol dehydratase]]		[[Category: Propanediol dehydratase]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]

OCA at 19:39, 19 September 2018

OCA — Wed, 19 Sep 2018 19:39:36 GMT

←Older revision		Revision as of 19:39, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yrt is ~~ON HOLD until Paper~~ Publication	+	==Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal==
		+	<StructureSection load='5yrt' size='340' side='right' caption='[[5yrt]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yrt]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YRT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] </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=5yrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrt OCA], [http://pdbe.org/5yrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrt RCSB], [http://www.ebi.ac.uk/pdbsum/5yrt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrt ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structures of the B12 -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.

-	~~Authors~~:	+	Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12 Catalysis.,Shibata N, Sueyoshi Y, Higuchi Y, Toraya T Angew Chem Int Ed Engl. 2018 Jun 25;57(26):7830-7835. doi:, 10.1002/anie.201803591. Epub 2018 May 25. PMID:29797764<ref>PMID:29797764</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yrt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Propanediol dehydratase]]
		+	[[Category: Shibata, N]]
		+	[[Category: Adenosylcobalamin]]
		+	[[Category: Lyase]]
		+	[[Category: Radical enzyme]]

OCA at 05:18, 14 June 2018

OCA — Thu, 14 Jun 2018 05:18:51 GMT

←Older revision		Revision as of 05:18, 14 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yrt is ON HOLD	+	The entry 5yrt is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5yrt" [edit=sysop:move=sysop]

OCA — Wed, 15 Nov 2017 06:18:39 GMT

Protected "5yrt" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yrt is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Nov 2017 06:18:38 GMT

New page: '''Unreleased structure''' The entry 5yrt is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yrt is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]