6bps - Revision history

OCA at 14:47, 4 October 2023

2023-10-04T14:47:53Z

← Older revision		Revision as of 14:47, 4 October 2023
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	<StructureSection load='6bps' size='340' side='right'caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6bps' size='340' side='right'caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BPS 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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=F2Y:3,5-DIFLUORO-L-TYROSINE'>F2Y</scene><~~/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=F2Y:3,5-DIFLUORO-L-TYROSINE'>F2Y</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=9606 HUMAN]~~)~~</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=6bps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bps OCA], [https://pdbe.org/6bps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bps RCSB], [https://www.ebi.ac.uk/pdbsum/6bps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bps ProSAT]</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=6bps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bps OCA], [~~http~~://pdbe.org/6bps PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bps RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bps PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bps ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/CDO1_HUMAN CDO1_HUMAN]] Initiates several important metabolic pathways related to pyruvate and several sulfurate compounds including sulfate, hypotaurine and taurine. Critical regulator of cellular cysteine concentrations. Has an important role in maintaining the hepatic concentation of intracellular free cysteine within a proper narrow range.		[https://www.uniprot.org/uniprot/CDO1_HUMAN CDO1_HUMAN] Initiates several important metabolic pathways related to pyruvate and several sulfurate compounds including sulfate, hypotaurine and taurine. Critical regulator of cellular cysteine concentrations. Has an important role in maintaining the hepatic concentation of intracellular free cysteine within a proper narrow range.
	<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: ~~Cysteine dioxygenase]]~~		[[Category: Homo sapiens]]
	~~[[Category: Human~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Li, J]]		[[Category: Li J]]
	[[Category: Liu, A]]		[[Category: Liu A]]
	[[Category: Shin, I]]		[[Category: Shin I]]
	~~[[Category: Cys-tyr cofactor]]~~
	~~[[Category: Cysteine]]~~
	~~[[Category: Iron]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Unnatural amino acid~~]]

OCA at 08:20, 27 November 2019

2019-11-27T08:20:00Z

← Older revision		Revision as of 08:20, 27 November 2019
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	==Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase==		==Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase==
	<StructureSection load='6bps' size='340' side='right' caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6bps' size='340' side='right'caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BPS FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6bps" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bps" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Cysteine dioxygenase]]		[[Category: Cysteine dioxygenase]]
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Li, J]]		[[Category: Li, J]]
	[[Category: Liu, A]]		[[Category: Liu, A]]

OCA at 06:11, 11 July 2018

2018-07-11T06:11:15Z

← Older revision		Revision as of 06:11, 11 July 2018
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	<StructureSection load='6bps' size='340' side='right' caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6bps' size='340' side='right' caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BPS 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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F2Y:3,5-DIFLUORO-L-TYROSINE'>F2Y</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F2Y:3,5-DIFLUORO-L-TYROSINE'>F2Y</scene></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=9606 HUMAN])</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=6bps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bps OCA], [http://pdbe.org/6bps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bps RCSB], [http://www.ebi.ac.uk/pdbsum/6bps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bps 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=6bps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bps OCA], [http://pdbe.org/6bps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bps RCSB], [http://www.ebi.ac.uk/pdbsum/6bps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bps ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CDO1_HUMAN CDO1_HUMAN]] Initiates several important metabolic pathways related to pyruvate and several sulfurate compounds including sulfate, hypotaurine and taurine. Critical regulator of cellular cysteine concentrations. Has an important role in maintaining the hepatic concentation of intracellular free cysteine within a proper narrow range.		[[http://www.uniprot.org/uniprot/CDO1_HUMAN CDO1_HUMAN]] Initiates several important metabolic pathways related to pyruvate and several sulfurate compounds including sulfate, hypotaurine and taurine. Critical regulator of cellular cysteine concentrations. Has an important role in maintaining the hepatic concentation of intracellular free cysteine within a proper narrow range.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and (19)F NMR, these data indicated that the enzyme could catalyze oxidative C-F or C-Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys-Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon-halogen bond activation.

			Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase.,Li J, Griffith WP, Davis I, Shin I, Wang J, Li F, Wang Y, Wherritt DJ, Liu A Nat Chem Biol. 2018 Jun 25. pii: 10.1038/s41589-018-0085-5. doi:, 10.1038/s41589-018-0085-5. PMID:29942080<ref>PMID:29942080</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6bps" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Cysteine dioxygenase]]		[[Category: Cysteine dioxygenase]]
			[[Category: Human]]
	[[Category: Li, J]]		[[Category: Li, J]]
	[[Category: Liu, A]]		[[Category: Liu, A]]

OCA at 07:11, 4 July 2018

2018-07-04T07:11:14Z

← Older revision		Revision as of 07:11, 4 July 2018
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6bps is ~~ON HOLD until Paper Publication~~		==Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase==
			<StructureSection load='6bps' size='340' side='right' caption='[[6bps]], [[Resolution\|resolution]] 2.10Å' scene=''>
	~~Authors~~: ~~Liu~~, A., Li, J., ~~Shin~~, I.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6bps]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BPS FirstGlance]. <br>
	~~Description~~: ~~Crystal structure~~ of cysteine~~-bound ferrous form~~ of ~~the uncrosslinked F2-Tyr157 human~~ cysteine ~~dioxygenase~~		</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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F2Y:3,5-DIFLUORO-L-TYROSINE'>F2Y</scene></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=6bps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bps OCA], [http://pdbe.org/6bps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bps RCSB], [http://www.ebi.ac.uk/pdbsum/6bps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bps ProSAT]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/CDO1_HUMAN CDO1_HUMAN]] Initiates several important metabolic pathways related to pyruvate and several sulfurate compounds including sulfate, hypotaurine and taurine. Critical regulator of cellular cysteine concentrations. Has an important role in maintaining the hepatic concentation of intracellular free cysteine within a proper narrow range.
			__TOC__
			</StructureSection>
			[[Category: Cysteine dioxygenase]]
	[[Category: Li, J]]		[[Category: Li, J]]
	[[Category: Liu, A]]		[[Category: Liu, A]]
	[[Category: Shin, I]]		[[Category: Shin, I]]
			[[Category: Cys-tyr cofactor]]
			[[Category: Cysteine]]
			[[Category: Iron]]
			[[Category: Oxidoreductase]]
			[[Category: Unnatural amino acid]]

OCA at 04:58, 20 December 2017

2017-12-20T04:58:57Z

← Older revision		Revision as of 04:58, 20 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6bps is ON HOLD		The entry 6bps is ON HOLD until Paper Publication

	Authors: Liu, A., Li, J., Shin, I.		Authors: Liu, A., Li, J., Shin, I.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Li, J]]		[[Category: Li, J]]
			[[Category: Liu, A]]
	[[Category: Shin, I]]		[[Category: Shin, I]]
	~~[[Category: Liu, A]]~~

OCA: Protected "6bps" [edit=sysop:move=sysop]

2017-12-06T06:04:30Z

Protected "6bps" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:04, 6 December 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6bps is ON HOLD Authors: Liu, A., Li, J., Shin, I. Description: Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 hum...

2017-12-06T06:04:29Z

New page: '''Unreleased structure''' The entry 6bps is ON HOLD Authors: Liu, A., Li, J., Shin, I. Description: Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 hum...

New page

'''Unreleased structure'''

The entry 6bps is ON HOLD

Authors: Liu, A., Li, J., Shin, I.

Description: Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase
[[Category: Unreleased Structures]]
[[Category: Li, J]]
[[Category: Shin, I]]
[[Category: Liu, A]]