3oul - Revision history

OCA at 11:18, 21 February 2024

OCA — Wed, 21 Feb 2024 11:18:56 GMT

←Older revision		Revision as of 11:18, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3oul' size='340' side='right'caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3oul' size='340' side='right'caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aerobacillus_polymyxa"_(prazmowski_1880)_donker_1926 "aerobacillus~~ polymyxa~~" (prazmowski 1880) donker 1926~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OUL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OUL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3oum\|3oum]]~~</~~div~~></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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [https://pdbe.org/3oul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [https://www.ebi.ac.uk/pdbsum/3oul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oul 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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [https://pdbe.org/3oul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [https://www.ebi.ac.uk/pdbsum/3oul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oul ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/E3SET7_PAEPO E3SET7_PAEPO]
-	Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 A in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis.	+
-		+
-	~~Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme.,Jung WS, Lee J, Kim MI, Ma J, Nagamatsu T, Goo E, Kim H, Hwang I, Han J, Rhee S PLoS One. 2011;6(7)~~:~~e22443. Epub 2011 Jul 25. PMID:21799856<ref>PMID:21799856<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3oul" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Kim, M I]]~~	+	[[Category: Paenibacillus polymyxa]]
-	~~[[Category: Rhee, S]]~~	+	[[Category: Kim MI]]
-	[[Category: Paenibacillus polymyxa ~~jh2~~]]	+	[[Category: Rhee S]]
-	[[Category: ~~Phytotoxin-degrading enzyme~~]]	+
-	[[Category: ~~Toxoflavin]]~~	+
-	~~[[Category: Toxoflavin binding protein]]~~	+
-	~~[[Category: Toxoflavin-degrading enzyme~~]]	+

OCA at 10:57, 18 May 2022

OCA — Wed, 18 May 2022 10:57:58 GMT

←Older revision		Revision as of 10:57, 18 May 2022
Line 1:		Line 1:

	==Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form==		==Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form==
-	<StructureSection load='3oul' size='340' side='right' caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3oul' size='340' side='right'caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aerobacillus_polymyxa"_(prazmowski_1880)_donker_1926 "aerobacillus polymyxa" (prazmowski 1880) donker 1926]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3OUL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacillus_polymyxa"_(prazmowski_1880)_donker_1926 "aerobacillus polymyxa" (prazmowski 1880) donker 1926]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OUL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oum\|3oum]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3oum\|3oum]]</div></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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [~~http~~://pdbe.org/3oul PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3oul PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3oul 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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [https://pdbe.org/3oul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [https://www.ebi.ac.uk/pdbsum/3oul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oul ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kim, M I]]		[[Category: Kim, M I]]
	[[Category: Rhee, S]]		[[Category: Rhee, S]]

OCA at 10:39, 5 August 2016

OCA — Fri, 05 Aug 2016 10:39:27 GMT

←Older revision		Revision as of 10:39, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form==		==Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form==
	<StructureSection load='3oul' size='340' side='right' caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3oul' size='340' side='right' caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Paenibacillus_polymyxa Paenibacillus~~ polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OUL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacillus_polymyxa"_(prazmowski_1880)_donker_1926 "aerobacillus polymyxa" (prazmowski 1880) donker 1926]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OUL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oum\|3oum]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oum\|3oum]]</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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [http://www.ebi.ac.uk/pdbsum/3oul 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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [http://pdbe.org/3oul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [http://www.ebi.ac.uk/pdbsum/3oul PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oul ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3oul" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Paenibacillus polymyxa]]
	[[Category: Kim, M I]]		[[Category: Kim, M I]]
	[[Category: Rhee, S]]		[[Category: Rhee, S]]

OCA at 21:15, 3 January 2015

OCA — Sat, 03 Jan 2015 21:15:34 GMT

←Older revision		Revision as of 21:15, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OUL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oum\|3oum]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oum\|3oum]]</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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [http://www.ebi.ac.uk/pdbsum/3oul 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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [http://www.ebi.ac.uk/pdbsum/3oul 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:
	Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme.,Jung WS, Lee J, Kim MI, Ma J, Nagamatsu T, Goo E, Kim H, Hwang I, Han J, Rhee S PLoS One. 2011;6(7):e22443. Epub 2011 Jul 25. PMID:21799856<ref>PMID:21799856</ref>		Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme.,Jung WS, Lee J, Kim MI, Ma J, Nagamatsu T, Goo E, Kim H, Hwang I, Han J, Rhee S PLoS One. 2011;6(7):e22443. Epub 2011 Jul 25. PMID:21799856<ref>PMID:21799856</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: Paenibacillus polymyxa]]		[[Category: Paenibacillus polymyxa]]
-	[[Category: Kim, M I.]]	+	[[Category: Kim, M I]]
-	[[Category: Rhee, S.]]	+	[[Category: Rhee, S]]
	[[Category: Paenibacillus polymyxa jh2]]		[[Category: Paenibacillus polymyxa jh2]]
	[[Category: Phytotoxin-degrading enzyme]]		[[Category: Phytotoxin-degrading enzyme]]

OCA at 10:26, 28 May 2014

OCA — Wed, 28 May 2014 10:26:57 GMT

←Older revision		Revision as of 10:26, 28 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3oul.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form==
		+	<StructureSection load='3oul' size='340' side='right' caption='[[3oul]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3oul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OUL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3oum\|3oum]]</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=3oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oul RCSB], [http://www.ebi.ac.uk/pdbsum/3oul PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 A in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis.

-	<!--	+	Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme.,Jung WS, Lee J, Kim MI, Ma J, Nagamatsu T, Goo E, Kim H, Hwang I, Han J, Rhee S PLoS One. 2011;6(7):e22443. Epub 2011 Jul 25. PMID:21799856<ref>PMID:21799856</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3oul"~~, ~~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_3oul\| PDB=3oul \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of ~~toxoflavin-degrading enzyme in a substrate-free form===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21799856}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21799856 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21799856}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3oul]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021799856<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Paenibacillus polymyxa]]		[[Category: Paenibacillus polymyxa]]
	[[Category: Kim, M I.]]		[[Category: Kim, M I.]]

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

OCA — Wed, 10 Aug 2011 06:00:47 GMT

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

←Older revision

Revision as of 06:00, 10 August 2011

OCA at 06:00, 10 August 2011

OCA — Wed, 10 Aug 2011 06:00:45 GMT

←Older revision		Revision as of 06:00, 10 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3oul.jpg\|left\|200px]]

-	The ~~entry 3oul~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3oul", 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_3oul\| PDB=3oul \| SCENE= }}

-	~~Authors: Kim, M.I., Rhee, S.~~	+	===Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form===

-	Description: Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Oct 6 05~~:49:~~17 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21799856}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21799856 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21799856}}
		+
		+	==About this Structure==
		+	[[3oul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OUL OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021799856</ref><references group="xtra"/>
		+	[[Category: Paenibacillus polymyxa]]
		+	[[Category: Kim, M I.]]
		+	[[Category: Rhee, S.]]
		+	[[Category: Paenibacillus polymyxa jh2]]
		+	[[Category: Phytotoxin-degrading enzyme]]
		+	[[Category: Toxoflavin]]
		+	[[Category: Toxoflavin binding protein]]
		+	[[Category: Toxoflavin-degrading enzyme]]

OCA at 02:39, 6 October 2010

OCA — Wed, 06 Oct 2010 02:39:46 GMT

←Older revision		Revision as of 02:39, 6 October 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Kim, M.I, Rhee, S	+	Authors: Kim, M.I., Rhee, S.

-	Description: Crystal Structure of toxoflavin-degrading enzyme	+	Description: Crystal Structure of toxoflavin-degrading enzyme in a substrate-free form

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 22 14~~:35:11 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 6 05:49:17 2010''

OCA: New page: '''Unreleased structure''' The entry 3oul is ON HOLD Authors: Kim, M.I, Rhee, S Description: Crystal Structure of toxoflavin-degrading enzyme ''Page seeded by [http://oca.weizmann.ac....

OCA — Wed, 22 Sep 2010 11:26:12 GMT

New page: '''Unreleased structure''' The entry 3oul is ON HOLD Authors: Kim, M.I, Rhee, S Description: Crystal Structure of toxoflavin-degrading enzyme ''Page seeded by [http://oca.weizmann.ac....

New page

'''Unreleased structure'''

The entry 3oul is ON HOLD

Authors: Kim, M.I, Rhee, S

Description: Crystal Structure of toxoflavin-degrading enzyme

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 14:35:11 2010''