5ko8 - Revision history

OCA at 10:49, 27 September 2023

OCA — Wed, 27 Sep 2023 10:49:43 GMT

←Older revision		Revision as of 10:49, 27 September 2023
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	==Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (I-Tyr)==		==Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (I-Tyr)==
-	<StructureSection load='5ko8' size='340' side='right' caption='[[5ko8]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5ko8' size='340' side='right'caption='[[5ko8]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ko8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Halh1 Halh1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KO8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ko8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haliscomenobacter_hydrossis_DSM_1100 Haliscomenobacter hydrossis DSM 1100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KO8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene~~>, ~~<scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</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]] 2.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5ko7\|5ko7]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Halhy_2296 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760192 HALH1])~~</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=5ko8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko8 OCA], [https://pdbe.org/5ko8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ko8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ko8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko8 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=5ko8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko8 OCA], [~~http~~://pdbe.org/5ko8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ko8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ko8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IYD_HALH1 IYD_HALH1] Catalyzes the dehalogenation of halotyrosines such as 3-iodo-L-tyrosine and 3,5-diiodo-L-tyrosine (PubMed:24153409, PubMed:28157283). Likely to also catalyze the dehalogenation of other halotyrosines such as 3-bromo-L-tyrosine, 3-chloro-L-tyrosine and 3-iodo-L-tyrosine (By similarity). Activity towards 3-iodo-L-tyrosine is much stronger than activity towards 3,5-diiodo-L-tyrosine and 2-iodophenol (PubMed:28157283, PubMed:24153409).[UniProtKB:B9K712]<ref>PMID:24153409</ref> <ref>PMID:28157283</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ko8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ko8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitroreductase 3D structures\|Nitroreductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halh1~~]]	+	[[Category: Haliscomenobacter hydrossis DSM 1100]]
-	[[Category: ~~Ingavat, N~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kavran, J M~~]]	+	[[Category: Ingavat N]]
-	[[Category: ~~Rokita, S E~~]]	+	[[Category: Kavran JM]]
-	[[Category: ~~Sun, Z~~]]	+	[[Category: Rokita SE]]
-	[[Category: ~~Flavin mononucleotide]]~~	+	[[Category: Sun Z]]
-	~~[[Category: Haliscomenobacter hydrossis]]~~	+
-	~~[[Category: Iodotyrosine deiodinase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 13:01, 6 November 2017

OCA — Mon, 06 Nov 2017 13:01:34 GMT

←Older revision		Revision as of 13:01, 6 November 2017
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	<StructureSection load='5ko8' size='340' side='right' caption='[[5ko8]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5ko8' size='340' side='right' caption='[[5ko8]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ko8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KO8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ko8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Halh1 Halh1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KO8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ko7\|5ko7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ko7\|5ko7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Halhy_2296 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760192 HALH1])</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=5ko8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko8 OCA], [http://pdbe.org/5ko8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ko8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ko8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko8 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=5ko8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko8 OCA], [http://pdbe.org/5ko8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ko8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ko8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko8 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Halh1]]
	[[Category: Ingavat, N]]		[[Category: Ingavat, N]]
	[[Category: Kavran, J M]]		[[Category: Kavran, J M]]

OCA at 08:27, 9 March 2017

OCA — Thu, 09 Mar 2017 08:27:03 GMT

←Older revision		Revision as of 08:27, 9 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5ko8 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (I-Tyr)==
		+	<StructureSection load='5ko8' size='340' side='right' caption='[[5ko8]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ko8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KO8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ko7\|5ko7]]</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=5ko8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko8 OCA], [http://pdbe.org/5ko8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ko8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ko8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The minimal requirements for substrate recognition and turnover by iodotyrosine deiodinase were examined to learn the basis for its catalytic specificity. This enzyme is crucial for iodide homeostasis and the generation of thyroid hormone in chordates. 2-Iodophenol binds only very weakly to the human enzyme and is dehalogenated with a kcat/Km that is more than 4 orders of magnitude lower than that for iodotyrosine. This discrimination likely protects against a futile cycle of iodinating and deiodinating precursors of thyroid hormone biosynthesis. Surprisingly, a very similar catalytic selectivity was expressed by a bacterial homologue from Haliscomenobacter hydrossis. In this example, discrimination was not based on affinity since 4-cyano-2-iodophenol bound to the bacterial deiodinase with a Kd lower than that of iodotyrosine and yet was not detectably deiodinated. Other phenols including 2-iodophenol were deiodinated but only very inefficiently. Crystal structures of the bacterial enzyme with and without bound iodotyrosine are nearly superimposable and quite similar to the corresponding structures of the human enzyme. Likewise, the bacterial enzyme is activated for single electron transfer after binding to the substrate analogue fluorotyrosine as previously observed with the human enzyme. A cocrystal structure of bacterial deiodinase and 2-iodophenol indicates that this ligand stacks on the active site flavin mononucleotide (FMN) in a orientation analogous to that of bound iodotyrosine. However, 2-iodophenol association is not sufficient to activate the FMN chemistry required for catalysis, and thus the bacterial enzyme appears to share a similar specificity for halotyrosines even though their physiological roles are likely very different from those in humans.

-	~~Authors~~:	+	Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase.,Ingavat N, Kavran JM, Sun Z, Rokita SE Biochemistry. 2017 Feb 28;56(8):1130-1139. doi: 10.1021/acs.biochem.6b01308. Epub, 2017 Feb 16. PMID:28157283<ref>PMID:28157283</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ko8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ingavat, N]]
		+	[[Category: Kavran, J M]]
		+	[[Category: Rokita, S E]]
		+	[[Category: Sun, Z]]
		+	[[Category: Flavin mononucleotide]]
		+	[[Category: Haliscomenobacter hydrossis]]
		+	[[Category: Iodotyrosine deiodinase]]
		+	[[Category: Oxidoreductase]]

OCA at 13:41, 3 October 2016

OCA — Mon, 03 Oct 2016 13:41:48 GMT

←Older revision		Revision as of 13:41, 3 October 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ko8 is ON HOLD	+	The entry 5ko8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 14:10, 9 September 2016

OCA — Fri, 09 Sep 2016 14:10:31 GMT

←Older revision		Revision as of 14:10, 9 September 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ko8 is ON HOLD ~~until Paper Publication~~	+	The entry 5ko8 is ON HOLD

	Authors:		Authors:

OCA at 13:36, 10 August 2016

OCA — Wed, 10 Aug 2016 13:36:04 GMT

←Older revision		Revision as of 13:36, 10 August 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ko8 is ON HOLD	+	The entry 5ko8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5ko8" [edit=sysop:move=sysop]

OCA — Wed, 13 Jul 2016 00:38:47 GMT

Protected "5ko8" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:38, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ko8 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Jul 2016 00:38:45 GMT

New page: '''Unreleased structure''' The entry 5ko8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ko8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]