4xfi - Revision history

OCA at 06:53, 3 April 2024

2024-04-03T06:53:21Z

←Older revision		Revision as of 06:53, 3 April 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CDO1_RAT CDO1_RAT]		[https://www.uniprot.org/uniprot/CDO1_RAT CDO1_RAT]
-	<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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4xfi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:45, 27 September 2023

2023-09-27T07:45:18Z

←Older revision		Revision as of 07:45, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XFI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XFI 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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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]] 1.4Å</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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [https://pdbe.org/4xfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [https://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi 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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [https://pdbe.org/4xfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [https://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:26, 12 April 2023

2023-04-12T21:26:32Z

←Older revision		Revision as of 21:26, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4xfi' size='340' side='right'caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4xfi' size='340' side='right'caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XFI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XFI 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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ieo\|4ieo]], [[4iep\|4iep]], [[4ieq\|4ieq]], [[4ier\|4ier]], [[4ies\|4ies]], [[4iet\|4iet]], [[4ieu\|4ieu]], [[4iev\|4iev]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4jtn\|4jtn]], [[4jto\|4jto]], [[4kwk\|4kwk]], [[4kwl\|4kwl]], [[4pix\|4pix]], [[4piy\|4piy]], [[4piz\|4piz]], [[4pjy\|4pjy]], [[4ext\|4ext]], [[4xez\|4xez]], [[4xf0\|4xf0]], [[4xf1\|4xf1]], [[4xf3\|4xf3]], [[4xf4\|4xf4]], [[4xf9\|4xf9]], [[4xfa\|4xfa]], [[4xfb\|4xfb]], [[4xfc\|4xfc]], [[4xff\|4xff]], [[4xfg\|4xfg]], [[4xfh\|4xfh]]</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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [https://pdbe.org/4xfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [https://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [~~http~~://pdbe.org/4xfi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi 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: ~~Cupin fold]]~~	+	[[Category: Karplus PA]]
-	~~[[Category: Cysteine to cysteine sulfinic acid catalysis]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Thiol dioxygenase~~]]	+

OCA at 08:44, 4 December 2019

2019-12-04T08:44:46Z

←Older revision		Revision as of 08:44, 4 December 2019
Line 1:		Line 1:

	==cysteine dioxygenase variant - Y157F at pH 6.2 with homocysteine==		==cysteine dioxygenase variant - Y157F at pH 6.2 with homocysteine==
-	<StructureSection load='4xfi' size='340' side='right' caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='4xfi' size='340' side='right'caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XFI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XFI FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4xfi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xfi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Buffalo rat]]		[[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 15:28, 15 November 2017

2017-11-15T15:28:39Z

←Older revision		Revision as of 15:28, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='4xfi' size='340' side='right' caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4xfi' size='340' side='right' caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xfi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XFI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XFI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xfi]] 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=4XFI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XFI 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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene></td></tr>		</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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ieo\|4ieo]], [[4iep\|4iep]], [[4ieq\|4ieq]], [[4ier\|4ier]], [[4ies\|4ies]], [[4iet\|4iet]], [[4ieu\|4ieu]], [[4iev\|4iev]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4jtn\|4jtn]], [[4jto\|4jto]], [[4kwk\|4kwk]], [[4kwl\|4kwl]], [[4pix\|4pix]], [[4piy\|4piy]], [[4piz\|4piz]], [[4pjy\|4pjy]], [[4ext\|4ext]], [[4xez\|4xez]], [[4xf0\|4xf0]], [[4xf1\|4xf1]], [[4xf3\|4xf3]], [[4xf4\|4xf4]], [[4xf9\|4xf9]], [[4xfa\|4xfa]], [[4xfb\|4xfb]], [[4xfc\|4xfc]], [[4xff\|4xff]], [[4xfg\|4xfg]], [[4xfh\|4xfh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ieo\|4ieo]], [[4iep\|4iep]], [[4ieq\|4ieq]], [[4ier\|4ier]], [[4ies\|4ies]], [[4iet\|4iet]], [[4ieu\|4ieu]], [[4iev\|4iev]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4jtn\|4jtn]], [[4jto\|4jto]], [[4kwk\|4kwk]], [[4kwl\|4kwl]], [[4pix\|4pix]], [[4piy\|4piy]], [[4piz\|4piz]], [[4pjy\|4pjy]], [[4ext\|4ext]], [[4xez\|4xez]], [[4xf0\|4xf0]], [[4xf1\|4xf1]], [[4xf3\|4xf3]], [[4xf4\|4xf4]], [[4xf9\|4xf9]], [[4xfa\|4xfa]], [[4xfb\|4xfb]], [[4xfc\|4xfc]], [[4xff\|4xff]], [[4xfg\|4xfg]], [[4xfh\|4xfh]]</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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [http://pdbe.org/4xfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [http://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi 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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [http://pdbe.org/4xfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [http://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Cysteine dioxygenase]]		[[Category: Cysteine dioxygenase]]
	[[Category: Driggers, C M]]		[[Category: Driggers, C M]]

OCA at 11:31, 15 December 2016

2016-12-15T11:31:41Z

←Older revision		Revision as of 11:31, 15 December 2016
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ieo\|4ieo]], [[4iep\|4iep]], [[4ieq\|4ieq]], [[4ier\|4ier]], [[4ies\|4ies]], [[4iet\|4iet]], [[4ieu\|4ieu]], [[4iev\|4iev]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4jtn\|4jtn]], [[4jto\|4jto]], [[4kwk\|4kwk]], [[4kwl\|4kwl]], [[4pix\|4pix]], [[4piy\|4piy]], [[4piz\|4piz]], [[4pjy\|4pjy]], [[4ext\|4ext]], [[4xez\|4xez]], [[4xf0\|4xf0]], [[4xf1\|4xf1]], [[4xf3\|4xf3]], [[4xf4\|4xf4]], [[4xf9\|4xf9]], [[4xfa\|4xfa]], [[4xfb\|4xfb]], [[4xfc\|4xfc]], [[4xff\|4xff]], [[4xfg\|4xfg]], [[4xfh\|4xfh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ieo\|4ieo]], [[4iep\|4iep]], [[4ieq\|4ieq]], [[4ier\|4ier]], [[4ies\|4ies]], [[4iet\|4iet]], [[4ieu\|4ieu]], [[4iev\|4iev]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4jtn\|4jtn]], [[4jto\|4jto]], [[4kwk\|4kwk]], [[4kwl\|4kwl]], [[4pix\|4pix]], [[4piy\|4piy]], [[4piz\|4piz]], [[4pjy\|4pjy]], [[4ext\|4ext]], [[4xez\|4xez]], [[4xf0\|4xf0]], [[4xf1\|4xf1]], [[4xf3\|4xf3]], [[4xf4\|4xf4]], [[4xf9\|4xf9]], [[4xfa\|4xfa]], [[4xfb\|4xfb]], [[4xfc\|4xfc]], [[4xff\|4xff]], [[4xfg\|4xfg]], [[4xfh\|4xfh]]</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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [http://pdbe.org/4xfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [http://www.ebi.ac.uk/pdbsum/4xfi PDBsum]</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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [http://pdbe.org/4xfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [http://www.ebi.ac.uk/pdbsum/4xfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfi ProSAT]</span></td></tr>
	</table>		</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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4xfi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:14, 26 February 2016

2016-02-26T18:14:45Z

←Older revision		Revision as of 18:14, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4xfi is ~~ON HOLD until Feb 19 2017~~	+	==cysteine dioxygenase variant - Y157F at pH 6.2 with homocysteine==
-		+	<StructureSection load='4xfi' size='340' side='right' caption='[[4xfi]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Driggers~~, C.M., ~~Karplus, P~~.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xfi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XFI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XFI FirstGlance]. <br>
-	~~Description~~: ~~cysteine dioxygenase variant~~ -~~Y157F at pH 6~~.~~2 with homocysteine~~	+	</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=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ieo\|4ieo]], [[4iep\|4iep]], [[4ieq\|4ieq]], [[4ier\|4ier]], [[4ies\|4ies]], [[4iet\|4iet]], [[4ieu\|4ieu]], [[4iev\|4iev]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4jtn\|4jtn]], [[4jto\|4jto]], [[4kwk\|4kwk]], [[4kwl\|4kwl]], [[4pix\|4pix]], [[4piy\|4piy]], [[4piz\|4piz]], [[4pjy\|4pjy]], [[4ext\|4ext]], [[4xez\|4xez]], [[4xf0\|4xf0]], [[4xf1\|4xf1]], [[4xf3\|4xf3]], [[4xf4\|4xf4]], [[4xf9\|4xf9]], [[4xfa\|4xfa]], [[4xfb\|4xfb]], [[4xfc\|4xfc]], [[4xff\|4xff]], [[4xfg\|4xfg]], [[4xfh\|4xfh]]</td></tr>
-	[[Category: Driggers, C.M]]	+	<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>
-	[[Category: Karplus, P.A]]	+	<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=4xfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfi OCA], [http://pdbe.org/4xfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xfi RCSB], [http://www.ebi.ac.uk/pdbsum/4xfi PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cysteine dioxygenase]]
		+	[[Category: Driggers, C M]]
		+	[[Category: Karplus, P A]]
		+	[[Category: Cupin fold]]
		+	[[Category: Cysteine to cysteine sulfinic acid catalysis]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Thiol dioxygenase]]

OCA at 23:09, 30 November 2015

2015-11-30T23:09:52Z

←Older revision		Revision as of 23:09, 30 November 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xfi is ON HOLD until ~~Paper Publication~~	+	The entry 4xfi is ON HOLD until Feb 19 2017

	Authors: Driggers, C.M., Karplus, P.A.		Authors: Driggers, C.M., Karplus, P.A.
Line 7:		Line 7:
	Description: cysteine dioxygenase variant -Y157F at pH 6.2 with homocysteine		Description: cysteine dioxygenase variant -Y157F at pH 6.2 with homocysteine
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Karplus, P.A]]
	[[Category: Driggers, C.M]]		[[Category: Driggers, C.M]]
		+	[[Category: Karplus, P.A]]

OCA at 14:26, 7 February 2015

2015-02-07T14:26:19Z

←Older revision		Revision as of 14:26, 7 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xfi is ON HOLD	+	The entry 4xfi is ON HOLD until Paper Publication

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

OCA: Protected "4xfi" [edit=sysop:move=sysop]

2015-01-07T15:36:14Z

Protected "4xfi" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:36, 7 January 2015