4iev - Revision history

OCA at 09:05, 9 November 2022

OCA — Wed, 09 Nov 2022 09:05:45 GMT

←Older revision		Revision as of 09:05, 9 November 2022
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	==Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys==		==Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys==
-	<StructureSection load='4iev' size='340' side='right' caption='[[4iev]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4iev' size='340' side='right'caption='[[4iev]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4iev]] 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=4IEV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4iev]] 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=4IEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IEV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4if0\|4if0]], [[4if1\|4if1]]</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=4iev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iev OCA], [https://pdbe.org/4iev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iev RCSB], [https://www.ebi.ac.uk/pdbsum/4iev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iev 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=4iev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iev OCA], [~~http~~://pdbe.org/4iev PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4iev RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4iev PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4iev 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 ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cysteine dioxygenase~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Cooley~~, R B~~]]	+	[[Category: Cooley RB]]
-	[[Category: Driggers~~, C M~~]]	+	[[Category: Driggers CM]]
-	[[Category: Karplus~~, P A]]~~	+	[[Category: Karplus PA]]
-	~~[[Category: C93-y157 crosslink]]~~	+
-	~~[[Category: Catalyzes oxidation]]~~	+
-	~~[[Category: Cupin fold]]~~	+
-	~~[[Category: Cysteine to cysteine sulfinate]]~~	+
-	~~[[Category: Cytosol]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 12:21, 11 August 2016

OCA — Thu, 11 Aug 2016 12:21:54 GMT

←Older revision		Revision as of 12:21, 11 August 2016
Line 1:		Line 1:
		+
	==Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys==		==Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys==
	<StructureSection load='4iev' size='340' side='right' caption='[[4iev]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4iev' size='340' side='right' caption='[[4iev]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4iev]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IEV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4iev]] 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=4IEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IEV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4if0\|4if0]], [[4if1\|4if1]]</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]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4if0\|4if0]], [[4if1\|4if1]]</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 ~~Rattus norvegicus~~])</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=4iev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iev RCSB], [http://www.ebi.ac.uk/pdbsum/4iev 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=4iev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iev OCA], [http://pdbe.org/4iev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4iev RCSB], [http://www.ebi.ac.uk/pdbsum/4iev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4iev ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4iev" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Cysteine dioxygenase]]		[[Category: Cysteine dioxygenase]]
-	[[Category: Rattus norvegicus]]
	[[Category: Cooley, R B]]		[[Category: Cooley, R B]]
	[[Category: Driggers, C M]]		[[Category: Driggers, C M]]

OCA at 14:32, 4 January 2015

OCA — Sun, 04 Jan 2015 14:32:02 GMT

←Older revision		Revision as of 14:32, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4iev\| PDB=4iev \| SCENE= }}~~	+	==Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys==
-	===Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys===	+	<StructureSection load='4iev' size='340' side='right' caption='[[4iev]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23747973}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4iev]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IEV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]], [[4iew\|4iew]], [[4iex\|4iex]], [[4iey\|4iey]], [[4iez\|4iez]], [[4if0\|4if0]], [[4if1\|4if1]]</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 Rattus norvegicus])</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=4iev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iev RCSB], [http://www.ebi.ac.uk/pdbsum/4iev PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes the conversion of cysteine (Cys) to cysteine sulfinic acid by an unclarified mechanism. One structural study revealed that a Cys-persulfenate (or Cys-persulfenic acid) formed in the active site, but quantum mechanical calculations have been used to support arguments that it is not an energetically feasible reaction intermediate. Here, we report a series of high-resolution structures of CDO soaked with Cys at pH values from 4 to 9. Cys binding is minimal at pH</=5 and persulfenate formation is consistently seen at pH values between 5.5 and 7. Also, a structure determined using laboratory-based X-ray diffraction shows that the persulfenate, with an apparent average O-O separation distance of ~1.8A, is not an artifact of synchrotron radiation. At pH>/=8, the active-site iron shifts from 4- to 5-coordinate, and Cys soaks reveal a complex with Cys, but no dioxygen, bound. This 'Cys-only' complex differs in detail from a previously published 'Cys-only' complex, which we reevaluate and conclude is not reliable. The high-resolution structures presented here do not resolve the CDO mechanism but do imply that an iron-bound persulfenate (or persulfenic acid) is energetically accessible in the CDO active site, and that CDO active-site chemistry in the crystals is influenced by protonation/deprotonation events with effective pKa values near ~5.5 and ~7.5 that influence Cys binding and oxygen binding/reactivity, respectively. Furthermore, this work provides reliable ligand-bound models for guiding future mechanistic considerations.

-	~~==About this Structure==~~	+	Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH.,Driggers CM, Cooley RB, Sankaran B, Hirschberger LL, Stipanuk MH, Karplus PA J Mol Biol. 2013 Jun 7. pii: S0022-2836(13)00358-6. doi:, 10.1016/j.jmb.2013.05.028. PMID:23747973<ref>PMID:23747973</ref>
-	~~[[4iev]] is a 1 chain structure with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4IEV OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023747973</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cysteine dioxygenase]]		[[Category: Cysteine dioxygenase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Cooley, R B.]]	+	[[Category: Cooley, R B]]
-	[[Category: Driggers, C M.]]	+	[[Category: Driggers, C M]]
-	[[Category: Karplus, P A.]]	+	[[Category: Karplus, P A]]
	[[Category: C93-y157 crosslink]]		[[Category: C93-y157 crosslink]]
	[[Category: Catalyzes oxidation]]		[[Category: Catalyzes oxidation]]

OCA at 10:15, 30 June 2013

OCA — Sun, 30 Jun 2013 10:15:32 GMT

←Older revision		Revision as of 10:15, 30 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4iev\| PDB=4iev \| SCENE= }}
		+	===Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys===
		+	{{ABSTRACT_PUBMED_23747973}}

-	~~The entry~~ 4iev is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4iev]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IEV OCA].

-	~~Authors~~: ~~Driggers, C.M.,~~ Cooley, R.B., Karplus, P.A.	+	==Reference==
-		+	<ref group="xtra">PMID:023747973</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Cys~~-~~only bound~~ Cysteine ~~Dioxygenase at pH 8.0 in the presence of Cys~~	+	[[Category: Cysteine dioxygenase]]
		+	[[Category: Rattus norvegicus]]
		+	[[Category: Cooley, R B.]]
		+	[[Category: Driggers, C M.]]
		+	[[Category: Karplus, P A.]]
		+	[[Category: C93-y157 crosslink]]
		+	[[Category: Catalyzes oxidation]]
		+	[[Category: Cupin fold]]
		+	[[Category: Cysteine to cysteine sulfinate]]
		+	[[Category: Cytosol]]
		+	[[Category: Oxidoreductase]]

OCA at 14:17, 27 February 2013

OCA — Wed, 27 Feb 2013 14:17:55 GMT

←Older revision		Revision as of 14:17, 27 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Driggers, C.M., Cooley, R.B., Karplus, P.A.		Authors: Driggers, C.M., Cooley, R.B., Karplus, P.A.

	Description: Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys		Description: Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys

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

OCA — Wed, 19 Dec 2012 11:09:42 GMT

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

←Older revision

Revision as of 11:09, 19 December 2012

OCA: New page: '''Unreleased structure''' The entry 4iev is ON HOLD Authors: Driggers, C.M., Cooley, R.B., Karplus, P.A. Description: Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of ...

OCA — Wed, 19 Dec 2012 11:09:41 GMT

New page: '''Unreleased structure''' The entry 4iev is ON HOLD Authors: Driggers, C.M., Cooley, R.B., Karplus, P.A. Description: Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of ...

New page

'''Unreleased structure'''

The entry 4iev is ON HOLD

Authors: Driggers, C.M., Cooley, R.B., Karplus, P.A.

Description: Cys-only bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys