5yrv - Revision history

OCA at 08:36, 22 November 2023

2023-11-22T08:36:16Z

←Older revision		Revision as of 08:36, 22 November 2023
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	<StructureSection load='5yrv' size='340' side='right'caption='[[5yrv]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5yrv' size='340' side='right'caption='[[5yrv]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrv]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YRV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrv]] 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=5YRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YRV 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>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</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]] 1.55Å</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>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</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=5yrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrv OCA], [~~http~~://pdbe.org/5yrv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yrv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yrv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrv 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=5yrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrv OCA], [https://pdbe.org/5yrv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yrv RCSB], [https://www.ebi.ac.uk/pdbsum/5yrv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrv 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

2020-10-21T09:26:35Z

←Older revision		Revision as of 09:26, 21 October 2020
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	==Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal==		==Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal==
-	<StructureSection load='5yrv' size='340' side='right' caption='[[5yrv]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5yrv' size='340' side='right'caption='[[5yrv]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrv]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YRV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrv]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YRV 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>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</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>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</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=5yrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrv OCA], [http://pdbe.org/5yrv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrv RCSB], [http://www.ebi.ac.uk/pdbsum/5yrv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrv 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=5yrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrv OCA], [http://pdbe.org/5yrv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrv RCSB], [http://www.ebi.ac.uk/pdbsum/5yrv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrv 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

2018-09-19T19:39:38Z

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

-	~~The entry~~ 5yrv is ~~ON HOLD until Paper~~ Publication	+	==Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal==
		+	<StructureSection load='5yrv' size='340' side='right' caption='[[5yrv]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yrv]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YRV 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>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</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=5yrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrv OCA], [http://pdbe.org/5yrv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrv RCSB], [http://www.ebi.ac.uk/pdbsum/5yrv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrv 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: Shibata~~, N.	+	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: Diol dehydratase, AdoCbl~~/1,2-~~propanediol, anaerobically~~-~~prepared crystal~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yrv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Propanediol dehydratase]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]
		+	[[Category: Adenosylcobalamin]]
		+	[[Category: Lyase]]
		+	[[Category: Radical enzyme]]

OCA at 04:56, 29 November 2017

2017-11-29T04:56:23Z

←Older revision		Revision as of 04:56, 29 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Shibata, N.		Authors: Shibata, N.

-	Description: Diol dehydratase, AdoCbl/~~substrate~~-~~free~~, anaerobically-prepared crystal	+	Description: Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]

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

2017-11-15T06:18:45Z

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

←Older revision

Revision as of 06:18, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yrv is ON HOLD Authors: Shibata, N. Description: Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal [[Category: Unreleased St...

2017-11-15T06:18:44Z

New page: '''Unreleased structure''' The entry 5yrv is ON HOLD Authors: Shibata, N. Description: Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 5yrv is ON HOLD

Authors: Shibata, N.

Description: Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal
[[Category: Unreleased Structures]]
[[Category: Shibata, N]]