5i0t - Revision history

OCA at 08:19, 23 August 2023

OCA — Wed, 23 Aug 2023 08:19:31 GMT

←Older revision		Revision as of 08:19, 23 August 2023
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	<StructureSection load='5i0t' size='340' side='right'caption='[[5i0t]], [[Resolution\|resolution]] 1.37Å' scene=''>		<StructureSection load='5i0t' size='340' side='right'caption='[[5i0t]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i0t]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i0t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I0T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=THJ:THIOSULFATE'>THJ</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]] 1.37Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=THJ:THIOSULFATE'>THJ</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i0r\|5i0r]]~~, ~~[[5i0s\|5i0s]], [[5i0u\|5i0u]]~~<~~/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=5i0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0t OCA], [https://pdbe.org/5i0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i0t RCSB], [https://www.ebi.ac.uk/pdbsum/5i0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0t ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">Cdo1~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat]~~)~~</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Cysteine_dioxygenase Cysteine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.20 1.13.11.20]~~ </~~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=5i0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0t OCA], [~~http~~://pdbe.org/5i0t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i0t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i0t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0t ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CDO1_RAT CDO1_RAT]
	<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: Buffalo rat]]
-	[[Category: Cysteine dioxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Driggers, C M~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Karplus, P A~~]]	+	[[Category: Driggers CM]]
-	[[Category: ~~Kean, K M~~]]	+	[[Category: Karplus PA]]
-	[[Category: ~~C93-y157 crosslink]]~~	+	[[Category: Kean KM]]
-	~~[[Category: Catalysis oxidation]]~~	+
-	~~[[Category: Cupin-fold]]~~	+
-	~~[[Category: Cysteine to cysteine sulfinate]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Thiosulfate~~]]	+

OCA at 08:40, 27 May 2020

OCA — Wed, 27 May 2020 08:40:05 GMT

←Older revision		Revision as of 08:40, 27 May 2020
Line 1:		Line 1:

	==Thiosulfate bound Cysteine Dioxygenase at pH 6.8==		==Thiosulfate bound Cysteine Dioxygenase at pH 6.8==
-	<StructureSection load='5i0t' size='340' side='right' caption='[[5i0t]], [[Resolution\|resolution]] 1.37Å' scene=''>	+	<StructureSection load='5i0t' size='340' side='right'caption='[[5i0t]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i0t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0T OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i0t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I0T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=THJ:THIOSULFATE'>THJ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=THJ:THIOSULFATE'>THJ</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i0r\|5i0r]], [[5i0s\|5i0s]], [[5i0u\|5i0u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i0r\|5i0r]], [[5i0s\|5i0s]], [[5i0u\|5i0u]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cdo1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_dioxygenase Cysteine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.20 1.13.11.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_dioxygenase Cysteine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.20 1.13.11.20] </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=5i0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0t OCA], [http://pdbe.org/5i0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i0t RCSB], [http://www.ebi.ac.uk/pdbsum/5i0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0t 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=5i0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0t OCA], [http://pdbe.org/5i0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i0t RCSB], [http://www.ebi.ac.uk/pdbsum/5i0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5i0t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i0t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Cysteine dioxygenase]]		[[Category: Cysteine dioxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Driggers, C M]]		[[Category: Driggers, C M]]
	[[Category: Karplus, P A]]		[[Category: Karplus, P A]]

OCA at 19:01, 15 December 2016

OCA — Thu, 15 Dec 2016 19:01:55 GMT

←Older revision		Revision as of 19:01, 15 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i0t is ~~ON HOLD until Paper~~ Publication	+	==Thiosulfate bound Cysteine Dioxygenase at pH 6.8==
		+	<StructureSection load='5i0t' size='340' side='right' caption='[[5i0t]], [[Resolution\|resolution]] 1.37Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i0t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I0T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=THJ:THIOSULFATE'>THJ</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i0r\|5i0r]], [[5i0s\|5i0s]], [[5i0u\|5i0u]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_dioxygenase Cysteine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.20 1.13.11.20] </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=5i0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i0t OCA], [http://pdbe.org/5i0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i0t RCSB], [http://www.ebi.ac.uk/pdbsum/5i0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i0t ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In mammals, the non-heme iron enzyme cysteine dioxygenase (CDO) helps regulate Cys levels through converting Cys to Cys sulfinic acid. Its activity is in part modulated by the formation of a Cys93-Tyr157 crosslink that increases its catalytic efficiency over 10-fold. Here, 21 high-resolution mammalian CDO structures are used to gain insight into how the Cys-Tyr crosslink promotes activity and how select competitive inhibitors bind. Crystal structures of crosslink-deficient C93A and Y157F variants reveal similar ~1.0-A shifts in the side chain of residue 157, and both variant structures have a new chloride ion coordinating the active site iron. Cys binding is also different from wild-type CDO, and no Cys-persulfenate forms in the C93A or Y157F active sites at pH6.2 or 8.0. We conclude that the crosslink enhances activity by positioning the Tyr157 hydroxyl to enable proper Cys binding, proper oxygen binding, and optimal chemistry. In addition, structures are presented for homocysteine (Hcy), D-Cys, thiosulfate, and azide bound as competitive inhibitors. The observed binding modes of Hcy and D-Cys clarify why they are not substrates, and the binding of azide shows that in contrast to what has been proposed, it does not bind in these crystals as a superoxide mimic.

-	~~Authors: Kean, K.M~~., Driggers, ~~C.M.~~, ~~Karplus~~, P.A.	+	Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase.,Driggers CM, Kean KM, Hirschberger LL, Cooley RB, Stipanuk MH, Karplus PA J Mol Biol. 2016 Oct 9;428(20):3999-4012. doi: 10.1016/j.jmb.2016.07.012. Epub, 2016 Jul 29. PMID:27477048<ref>PMID:27477048</ref>

-	~~Description: Thiosulfate bound Cysteine Dioxygenase at pH 6~~.8	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Kean~~, K.M]]	+	<div class="pdbe-citations 5i0t" style="background-color:#fffaf0;"></div>
-	[[Category: Karplus, P.A]]	+	== References ==
-	[[Category: ~~Driggers~~, C.M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cysteine dioxygenase]]
		+	[[Category: Driggers, C M]]
		+	[[Category: Karplus, P A]]
		+	[[Category: Kean, K M]]
		+	[[Category: C93-y157 crosslink]]
		+	[[Category: Catalysis oxidation]]
		+	[[Category: Cupin-fold]]
		+	[[Category: Cysteine to cysteine sulfinate]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Thiosulfate]]

OCA at 13:14, 2 March 2016

OCA — Wed, 02 Mar 2016 13:14:22 GMT

←Older revision		Revision as of 13:14, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i0t is ON HOLD	+	The entry 5i0t is ON HOLD until Paper Publication

	Authors: Kean, K.M., Driggers, C.M., Karplus, P.A.		Authors: Kean, K.M., Driggers, C.M., Karplus, P.A.

OCA: Protected "5i0t" [edit=sysop:move=sysop]

OCA — Wed, 10 Feb 2016 16:02:19 GMT

Protected "5i0t" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:02, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i0t is ON HOLD Authors: Kean, K.M., Driggers, C.M., Karplus, P.A. Description: Thiosulfate bound Cysteine Dioxygenase at pH 6.8 [[Category: Unrele...

OCA — Wed, 10 Feb 2016 16:02:17 GMT

New page: '''Unreleased structure''' The entry 5i0t is ON HOLD Authors: Kean, K.M., Driggers, C.M., Karplus, P.A. Description: Thiosulfate bound Cysteine Dioxygenase at pH 6.8 [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5i0t is ON HOLD

Authors: Kean, K.M., Driggers, C.M., Karplus, P.A.

Description: Thiosulfate bound Cysteine Dioxygenase at pH 6.8
[[Category: Unreleased Structures]]
[[Category: Kean, K.M]]
[[Category: Karplus, P.A]]
[[Category: Driggers, C.M]]