6edh - Revision history

OCA at 14:40, 13 March 2024

OCA — Wed, 13 Mar 2024 14:40:48 GMT

←Older revision		Revision as of 14:40, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6edh]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EDH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6edh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EDH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</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]] 1.7300041Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tauD, ssiD, yaiG, b0368, JW0360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Taurine_dioxygenase Taurine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.17 1.14.11.17] </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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [https://pdbe.org/6edh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [https://www.ebi.ac.uk/pdbsum/6edh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh 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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [~~http~~://pdbe.org/6edh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6edh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI]] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme.	+	[https://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Iron(II)- and 2-(oxo)-glutarate-dependent (Fe/2OG) oxygenases catalyze a diverse array of oxidation reactions via a common iron(IV)-oxo (ferryl) intermediate. Although the intermediate has been characterized spectroscopically, its short lifetime has precluded crystallograhic characterization. In solution, the ferryl was first observed directly in the archetypal Fe/2OG hydroxylase, taurine:2OG dioxygenase (TauD). Here, we substitute the iron cofactor of TauD with the stable vanadium(IV)-oxo (vanadyl) ion to obtain crystal structures mimicking the key ferryl complex. Intriguingly, whereas the structure of the TauD.(V(IV)-oxo).succinate.taurine complex exhibits the expected orientation of the V identical withO bond-trans to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD.(V(IV)-oxo) binary complex is best modeled with its oxo ligand trans to Asp101. This off-line-like configuration is similar to one recently posited as a means to avoid hydroxylation in Fe/2OG enzymes that direct other outcomes, though neither has been visualized in an Fe/2OG structure to date. Whereas an off-line (trans to the proximal His) or off-line-like (trans to the carboxylate ligand) ferryl is unlikely to be important in the hydroxylation reaction of TauD, the observation that the ferryl may deviate from an in-line orientation in the absence of the primary substrate may explain the enzyme's mysterious self-hydroxylation behavior, should the oxo ligand lie trans to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases.	+

-	Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.,Davis KM, Altmyer M, Martinie RJ, Schaperdoth I, Krebs C, Bollinger JM Jr, Boal AK Biochemistry. 2019 Oct 15;58(41):4218-4223. doi: 10.1021/acs.biochem.9b00598., Epub 2019 Oct 2. PMID:31503454<ref>PMID:31503454</ref>	+	==See Also==
-		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6edh" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Taurine dioxygenase]]~~	+	[[Category: Altmyer M]]
-	[[Category: Altmyer, M]]	+	[[Category: Boal AK]]
-	[[Category: Boal~~, A K~~]]	+	[[Category: Davis KM]]
-	[[Category: Davis~~, K M]]~~	+
-	~~[[Category: 2-oxo-glutarate]]~~	+
-	~~[[Category: Hydroxylase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Vanadyl ion~~]]	+

OCA at 07:50, 23 October 2019

OCA — Wed, 23 Oct 2019 07:50:43 GMT

←Older revision		Revision as of 07:50, 23 October 2019
Line 3:		Line 3:
	<StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6edh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6edh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tauD, ssiD, yaiG, b0368, JW0360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Taurine_dioxygenase Taurine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.17 1.14.11.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Taurine_dioxygenase Taurine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.17 1.14.11.17] </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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [http://pdbe.org/6edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [http://www.ebi.ac.uk/pdbsum/6edh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh 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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [http://pdbe.org/6edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [http://www.ebi.ac.uk/pdbsum/6edh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI]] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme.		[[http://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI]] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Iron(II)- and 2-(oxo)-glutarate-dependent (Fe/2OG) oxygenases catalyze a diverse array of oxidation reactions via a common iron(IV)-oxo (ferryl) intermediate. Although the intermediate has been characterized spectroscopically, its short lifetime has precluded crystallograhic characterization. In solution, the ferryl was first observed directly in the archetypal Fe/2OG hydroxylase, taurine:2OG dioxygenase (TauD). Here, we substitute the iron cofactor of TauD with the stable vanadium(IV)-oxo (vanadyl) ion to obtain crystal structures mimicking the key ferryl complex. Intriguingly, whereas the structure of the TauD.(V(IV)-oxo).succinate.taurine complex exhibits the expected orientation of the V identical withO bond-trans to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD.(V(IV)-oxo) binary complex is best modeled with its oxo ligand trans to Asp101. This off-line-like configuration is similar to one recently posited as a means to avoid hydroxylation in Fe/2OG enzymes that direct other outcomes, though neither has been visualized in an Fe/2OG structure to date. Whereas an off-line (trans to the proximal His) or off-line-like (trans to the carboxylate ligand) ferryl is unlikely to be important in the hydroxylation reaction of TauD, the observation that the ferryl may deviate from an in-line orientation in the absence of the primary substrate may explain the enzyme's mysterious self-hydroxylation behavior, should the oxo ligand lie trans to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases.
		+
		+	Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.,Davis KM, Altmyer M, Martinie RJ, Schaperdoth I, Krebs C, Bollinger JM Jr, Boal AK Biochemistry. 2019 Oct 15;58(41):4218-4223. doi: 10.1021/acs.biochem.9b00598., Epub 2019 Oct 2. PMID:31503454<ref>PMID:31503454</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6edh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Taurine dioxygenase]]		[[Category: Taurine dioxygenase]]

OCA at 05:50, 21 August 2019

OCA — Wed, 21 Aug 2019 05:50:30 GMT

←Older revision		Revision as of 05:50, 21 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6edh is ~~ON HOLD until Paper Publication~~	+	==Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate==
-		+	<StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution\|resolution]] 1.73Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6edh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDH FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Taurine_dioxygenase Taurine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.17 1.14.11.17] </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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [http://pdbe.org/6edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [http://www.ebi.ac.uk/pdbsum/6edh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI]] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Taurine dioxygenase]]
		+	[[Category: Altmyer, M]]
		+	[[Category: Boal, A K]]
		+	[[Category: Davis, K M]]
		+	[[Category: 2-oxo-glutarate]]
		+	[[Category: Hydroxylase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Vanadyl ion]]

OCA at 05:44, 29 August 2018

OCA — Wed, 29 Aug 2018 05:44:25 GMT

←Older revision		Revision as of 05:44, 29 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6edh is ON HOLD	+	The entry 6edh is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 15 Aug 2018 14:56:44 GMT

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

←Older revision

Revision as of 14:56, 15 August 2018

OCA: New page: '''Unreleased structure''' The entry 6edh is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Aug 2018 14:56:43 GMT

New page: '''Unreleased structure''' The entry 6edh is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6edh is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]