3rna - Revision history

OCA at 12:30, 14 March 2024

OCA — Thu, 14 Mar 2024 12:30:35 GMT

←Older revision		Revision as of 12:30, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3rna' size='340' side='right'caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3rna' size='340' side='right'caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp.~~_ox1~~ Pseudomonas sp. ~~ox1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RNA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._OX1 Pseudomonas sp. OX1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RNA 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=OH:HYDROXIDE+ION'>OH</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]] 3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]~~</~~div~~><~~/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=OH:HYDROXIDE+ION'>OH</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">touA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [https://pdbe.org/3rna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [https://www.ebi.ac.uk/pdbsum/3rna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rna 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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [https://pdbe.org/3rna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [https://www.ebi.ac.uk/pdbsum/3rna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rna ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q6IV66_9PSED Q6IV66_9PSED]
-	For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/o-xylene monooxygenase hydroxylase is a dioxygen-activating enzyme. Structural analysis suggests two possible pathways for dioxygen access through the alpha-subunit to the diiron center: a channel or a series of hydrophobic cavities. To distinguish which is utilized as the O(2) migration pathway, the dimensions of the cavities and the channel were independently varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate constants for dioxygen access to the diiron center were derived from the formation rates of a peroxodiiron(III) intermediate, generated upon treatment of the diiron(II) enzyme with O(2). This reaction depends on the concentration of dioxygen to the first order. Altering the dimensions of the cavities, but not the channel, changed the rate of dioxygen reactivity with the enzyme. These results strongly suggest that voids comprising the cavities in toluene/~~o-xylene monooxygenase hydroxylase are not artifacts of protein packing~~/~~folding, but rather programmed routes for dioxygen migration through the protein matrix~~. ~~Because the cavities are not fully connected into the diiron active center in the enzyme resting state, conformational changes will be required to facilitate dioxygen access to the diiron center~~. We propose that such temporary opening and closing of the cavities may occur in all bacterial multicomponent monooxygenases to control O(2) consumption for efficient catalysis. Our findings suggest that other gas-utilizing enzymes may employ similar structural features to effect substrate passage through a protein matrix.	+
-		+
-	~~Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.,Song WJ, Gucinski G, Sazinsky MH, Lippard SJ Proc Natl Acad Sci U S A. 2011 Aug 22. PMID:21859951<ref>PMID:21859951<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rna" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]		*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pseudomonas sp. ~~ox1~~]]	+	[[Category: Pseudomonas sp. OX1]]
-	[[Category: Gucinski, G]]	+	[[Category: Gucinski G]]
-	[[Category: Lippard~~, S J~~]]	+	[[Category: Lippard SJ]]
-	[[Category: Sazinsky~~, M H~~]]	+	[[Category: Sazinsky MH]]
-	[[Category: Song~~, W J]]~~	+	[[Category: Song WJ]]
-	~~[[Category: Diiron]]~~	+
-	~~[[Category: Four-helix bundle]]~~	+
-	~~[[Category: Hydroxylase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxygen pathway]]~~	+
-	~~[[Category: Toluene~~]]	+

OCA at 10:18, 22 June 2022

OCA — Wed, 22 Jun 2022 10:18:18 GMT

←Older revision		Revision as of 10:18, 22 June 2022
Line 1:		Line 1:

	==Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant==		==Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant==
-	<StructureSection load='3rna' size='340' side='right' caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='3rna' size='340' side='right'caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RNA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RNA 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=OH:HYDROXIDE+ION'>OH</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=OH:HYDROXIDE+ION'>OH</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [~~http~~://pdbe.org/3rna PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rna PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rna 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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [https://pdbe.org/3rna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [https://www.ebi.ac.uk/pdbsum/3rna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rna ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 3rna" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3rna" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pseudomonas sp. ox1]]		[[Category: Pseudomonas sp. ox1]]
	[[Category: Gucinski, G]]		[[Category: Gucinski, G]]

OCA at 13:17, 11 August 2016

OCA — Thu, 11 Aug 2016 13:17:51 GMT

←Older revision		Revision as of 13:17, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant==		==Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant==
	<StructureSection load='3rna' size='340' side='right' caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3rna' size='340' side='right' caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [http://www.ebi.ac.uk/pdbsum/3rna 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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [http://pdbe.org/3rna PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [http://www.ebi.ac.uk/pdbsum/3rna PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rna ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3rna" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:14, 4 January 2015

OCA — Sun, 04 Jan 2015 10:14:28 GMT

←Older revision		Revision as of 10:14, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RNA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RNA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene><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=OH:HYDROXIDE+ION'>OH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [http://www.ebi.ac.uk/pdbsum/3rna 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=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [http://www.ebi.ac.uk/pdbsum/3rna PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.,Song WJ, Gucinski G, Sazinsky MH, Lippard SJ Proc Natl Acad Sci U S A. 2011 Aug 22. PMID:21859951<ref>PMID:21859951</ref>		Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.,Song WJ, Gucinski G, Sazinsky MH, Lippard SJ Proc Natl Acad Sci U S A. 2011 Aug 22. PMID:21859951<ref>PMID:21859951</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas sp. ox1]]		[[Category: Pseudomonas sp. ox1]]
-	[[Category: Gucinski, G.]]	+	[[Category: Gucinski, G]]
-	[[Category: Lippard, S J.]]	+	[[Category: Lippard, S J]]
-	[[Category: Sazinsky, M H.]]	+	[[Category: Sazinsky, M H]]
-	[[Category: Song, W J.]]	+	[[Category: Song, W J]]
	[[Category: Diiron]]		[[Category: Diiron]]
	[[Category: Four-helix bundle]]		[[Category: Four-helix bundle]]

OCA at 04:40, 5 June 2014

OCA — Thu, 05 Jun 2014 04:40:27 GMT

←Older revision		Revision as of 04:40, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3rna.~~png~~\|~~left~~\|~~200px~~]]	+	==Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant==
		+	<StructureSection load='3rna' size='340' side='right' caption='[[3rna]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rna]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RNA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rn9\|3rn9]], [[3rnb\|3rnb]], [[3rnc\|3rnc]], [[3rne\|3rne]], [[3rnf\|3rnf]], [[3rng\|3rng]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rna OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rna RCSB], [http://www.ebi.ac.uk/pdbsum/3rna PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/o-xylene monooxygenase hydroxylase is a dioxygen-activating enzyme. Structural analysis suggests two possible pathways for dioxygen access through the alpha-subunit to the diiron center: a channel or a series of hydrophobic cavities. To distinguish which is utilized as the O(2) migration pathway, the dimensions of the cavities and the channel were independently varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate constants for dioxygen access to the diiron center were derived from the formation rates of a peroxodiiron(III) intermediate, generated upon treatment of the diiron(II) enzyme with O(2). This reaction depends on the concentration of dioxygen to the first order. Altering the dimensions of the cavities, but not the channel, changed the rate of dioxygen reactivity with the enzyme. These results strongly suggest that voids comprising the cavities in toluene/o-xylene monooxygenase hydroxylase are not artifacts of protein packing/folding, but rather programmed routes for dioxygen migration through the protein matrix. Because the cavities are not fully connected into the diiron active center in the enzyme resting state, conformational changes will be required to facilitate dioxygen access to the diiron center. We propose that such temporary opening and closing of the cavities may occur in all bacterial multicomponent monooxygenases to control O(2) consumption for efficient catalysis. Our findings suggest that other gas-utilizing enzymes may employ similar structural features to effect substrate passage through a protein matrix.

-	<!--	+	Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.,Song WJ, Gucinski G, Sazinsky MH, Lippard SJ Proc Natl Acad Sci U S A. 2011 Aug 22. PMID:21859951<ref>PMID:21859951</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3rna"~~, ~~creates the "Structure Box" on the page.~~	+
-	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded)~~,	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3rna\| PDB=3rna \| SCENE= }}~~	+

-	~~===Structure of the Toluene~~/~~o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21859951}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21859951 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21859951}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3rna]] is a 3 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021859951<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pseudomonas sp. ox1]]		[[Category: Pseudomonas sp. ox1]]
	[[Category: Gucinski, G.]]		[[Category: Gucinski, G.]]

OCA at 05:21, 7 September 2011

OCA — Wed, 07 Sep 2011 05:21:46 GMT

←Older revision		Revision as of 05:21, 7 September 2011
Line 1:		Line 1:
-	[[Image:3rna.~~jpg~~\|left\|200px]]	+	[[Image:3rna.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant===		===Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21859951}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21859951 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21859951}}

	==About this Structure==		==About this Structure==
	[[3rna]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA].		[[3rna]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021859951</ref><references group="xtra"/>
	[[Category: Pseudomonas sp. ox1]]		[[Category: Pseudomonas sp. ox1]]
	[[Category: Gucinski, G.]]		[[Category: Gucinski, G.]]

OCA at 06:30, 17 August 2011

OCA — Wed, 17 Aug 2011 06:30:07 GMT

←Older revision		Revision as of 06:30, 17 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rna.jpg\|left\|200px]]

-	The ~~entry 3rna~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rna", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3rna\| PDB=3rna \| SCENE= }}

-	~~Authors: Gucinski, G., Song, W.J., Lippard, S.J., Sazinsky, M.H.~~	+	===Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant===

-	~~Description:~~ Structure ~~of the Toluene~~/o-~~Xylene Monooxygenase Hydroxylase T201S~~/~~I100W Double Mutant~~	+
		+	==About this Structure==
		+	[[3rna]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNA OCA].
		+	[[Category: Pseudomonas sp. ox1]]
		+	[[Category: Gucinski, G.]]
		+	[[Category: Lippard, S J.]]
		+	[[Category: Sazinsky, M H.]]
		+	[[Category: Song, W J.]]
		+	[[Category: Diiron]]
		+	[[Category: Four-helix bundle]]
		+	[[Category: Hydroxylase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygen pathway]]
		+	[[Category: Toluene]]

OCA at 05:13, 18 May 2011

OCA — Wed, 18 May 2011 05:13:51 GMT

←Older revision		Revision as of 05:13, 18 May 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rna is ON HOLD	+	The entry 3rna is ON HOLD until Paper Publication

	Authors: Gucinski, G., Song, W.J., Lippard, S.J., Sazinsky, M.H.		Authors: Gucinski, G., Song, W.J., Lippard, S.J., Sazinsky, M.H.

	Description: Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant		Description: Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant

OCA: Protected "3rna" [edit=sysop:move=sysop]

OCA — Wed, 04 May 2011 06:33:24 GMT

Protected "3rna" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:33, 4 May 2011

OCA: New page: '''Unreleased structure''' The entry 3rna is ON HOLD Authors: Gucinski, G., Song, W.J., Lippard, S.J., Sazinsky, M.H. Description: Structure of the Toluene/o-Xylene Monooxygenase Hydro...

OCA — Wed, 04 May 2011 06:33:23 GMT

New page: '''Unreleased structure''' The entry 3rna is ON HOLD Authors: Gucinski, G., Song, W.J., Lippard, S.J., Sazinsky, M.H. Description: Structure of the Toluene/o-Xylene Monooxygenase Hydro...

New page

'''Unreleased structure'''

The entry 3rna is ON HOLD

Authors: Gucinski, G., Song, W.J., Lippard, S.J., Sazinsky, M.H.

Description: Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W Double Mutant