3gb4 - Revision history

OCA at 09:53, 21 February 2024

OCA — Wed, 21 Feb 2024 09:53:43 GMT

←Older revision		Revision as of 09:53, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3gb4' size='340' side='right'caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3gb4' size='340' side='right'caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"pseudomonas_maltophilia"_hugh_and_ryschenkow_1961 "pseudomonas~~ maltophilia~~" hugh and ryschenkow 1961~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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]] 2.05Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [https://pdbe.org/3gb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [https://www.ebi.ac.uk/pdbsum/3gb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gb4 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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [https://pdbe.org/3gb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [https://www.ebi.ac.uk/pdbsum/3gb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gb4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DDMC_STEMA DDMC_STEMA] Component of the dicamba O-demethylase multicomponent enzyme system involved in the degradation of the herbicide dicamba (PubMed:15855162, PubMed:15820213, PubMed:16535584). In vitro, catalyzes the O-demethylation of 2-methoxy-3,6-dichlorobenzoic acid (dicamba) to yield 3,6-dichlorosalicylic acid (DCSA) via an exocyclic monooxygenation (PubMed:15855162, PubMed:15820213, PubMed:16535584, PubMed:19616009).<ref>PMID:15820213</ref> <ref>PMID:15855162</ref> <ref>PMID:16535584</ref> <ref>PMID:19616009</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gb4 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gb4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Dicamba (2-methoxy-3,6-dichlorobenzoic acid) O-demethylase (DMO) is the terminal Rieske oxygenase of a three-component system that includes a ferredoxin and a reductase. It catalyzes the NADH-dependent oxidative demethylation of the broad leaf herbicide dicamba. DMO represents the first crystal structure of a Rieske non-heme iron oxygenase that performs an exocyclic monooxygenation, incorporating O(2) into a side-chain moiety and not a ring system. The structure reveals a 3-fold symmetric trimer (alpha(3)) in the crystallographic asymmetric unit with similar arrangement of neighboring inter-subunit Rieske domain and non-heme iron site enabling electron transport consistent with other structurally characterized Rieske oxygenases. While the Rieske domain is similar, differences are observed in the catalytic domain, which is smaller in sequence length than those described previously, yet possessing an active-site cavity of larger volume when compared to oxygenases with larger substrates. Consistent with the amphipathic substrate, the active site is designed to interact with both the carboxylate and aromatic ring with both key polar and hydrophobic interactions observed. DMO structures were solved with and without substrate (dicamba), product (3,6-dichlorosalicylic acid), and either cobalt or iron in the non-heme iron site. The substitution of cobalt for iron revealed an uncommon mode of non-heme iron binding trapped by the non-catalytic Co(2+), which, we postulate, may be transiently present in the native enzyme during the catalytic cycle. Thus, we present four DMO structures with resolutions ranging from 1.95 to 2.2 A, which, in sum, provide a snapshot of a dynamic enzyme where metal binding and substrate binding are coupled to observed structural changes in the non-heme iron and catalytic sites.
-
-	Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation.,D'Ordine RL, Rydel TJ, Storek MJ, Sturman EJ, Moshiri F, Bartlett RK, Brown GR, Eilers RJ, Dart C, Qi Y, Flasinski S, Franklin SJ J Mol Biol. 2009 Sep 18;392(2):481-97. Epub 2009 Jul 15. PMID:19616009<ref>PMID:19616009</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3gb4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pseudomonas maltophilia hugh and ryschenkow 1961]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brown~~, G R~~]]	+	[[Category: Stenotrophomonas maltophilia]]
-	[[Category: Moshiri, F]]	+	[[Category: Brown GR]]
-	[[Category: Qi, Y]]	+	[[Category: Moshiri F]]
-	[[Category: Rydel~~, T J~~]]	+	[[Category: Qi Y]]
-	[[Category: Sturman~~, E J]]~~	+	[[Category: Rydel TJ]]
-	~~[[Category: 2fe-2]]~~	+	[[Category: Sturman EJ]]
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Iron-sulfur]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rieske non-heme iron oxygenase~~]]	+

OCA at 20:04, 20 October 2021

OCA — Wed, 20 Oct 2021 20:04:14 GMT

←Older revision		Revision as of 20:04, 20 October 2021
Line 1:		Line 1:

	==Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba==		==Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba==
-	<StructureSection load='3gb4' size='340' side='right' caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='3gb4' size='340' side='right'caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"pseudomonas_maltophilia"_hugh_and_ryschenkow_1961 "pseudomonas maltophilia" hugh and ryschenkow 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_maltophilia"_hugh_and_ryschenkow_1961 "pseudomonas maltophilia" hugh and ryschenkow 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [~~http~~://pdbe.org/3gb4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gb4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gb4 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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [https://pdbe.org/3gb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [https://www.ebi.ac.uk/pdbsum/3gb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gb4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gb/3gb4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gb/3gb4_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas maltophilia hugh and ryschenkow 1961]]		[[Category: Pseudomonas maltophilia hugh and ryschenkow 1961]]
		+	[[Category: Large Structures]]
	[[Category: Brown, G R]]		[[Category: Brown, G R]]
	[[Category: Moshiri, F]]		[[Category: Moshiri, F]]

OCA at 07:01, 1 November 2017

OCA — Wed, 01 Nov 2017 07:01:58 GMT

←Older revision		Revision as of 07:01, 1 November 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba==		==Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba==
	<StructureSection load='3gb4' size='340' side='right' caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3gb4' size='340' side='right' caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [http://pdbe.org/3gb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [http://www.ebi.ac.uk/pdbsum/3gb4 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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [http://pdbe.org/3gb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [http://www.ebi.ac.uk/pdbsum/3gb4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gb4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	[[Category: Rydel, T J]]		[[Category: Rydel, T J]]
	[[Category: Sturman, E J]]		[[Category: Sturman, E J]]
		+	[[Category: 2fe-2]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 20:44, 9 February 2016

OCA — Tue, 09 Feb 2016 20:44:33 GMT

←Older revision		Revision as of 20:44, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3gb4' size='340' side='right' caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3gb4' size='340' side='right' caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Stenotrophomonas_maltophilia Stenotrophomonas~~ maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_maltophilia"_hugh_and_ryschenkow_1961 "pseudomonas maltophilia" hugh and ryschenkow 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 ~~Stenotrophomonas~~ maltophilia])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [http://www.ebi.ac.uk/pdbsum/3gb4 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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [http://pdbe.org/3gb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [http://www.ebi.ac.uk/pdbsum/3gb4 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gb4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3gb4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Stenotrophomonas~~ maltophilia]]	+	[[Category: Pseudomonas maltophilia hugh and ryschenkow 1961]]
	[[Category: Brown, G R]]		[[Category: Brown, G R]]
	[[Category: Moshiri, F]]		[[Category: Moshiri, F]]

OCA at 13:56, 18 December 2014

OCA — Thu, 18 Dec 2014 13:56:28 GMT

←Older revision		Revision as of 13:56, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3gb4\| PDB=3gb4 \| SCENE= }}~~	+	==Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba==
-	===Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba===	+	<StructureSection load='3gb4' size='340' side='right' caption='[[3gb4]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19616009}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gb4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GB4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=D3M:3,6-DICHLORO-2-METHOXYBENZOIC+ACID'>D3M</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gob\|3gob]], [[3gts\|3gts]], [[3gte\|3gte]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddmC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 Stenotrophomonas maltophilia])</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=3gb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gb4 RCSB], [http://www.ebi.ac.uk/pdbsum/3gb4 PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gb/3gb4_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dicamba (2-methoxy-3,6-dichlorobenzoic acid) O-demethylase (DMO) is the terminal Rieske oxygenase of a three-component system that includes a ferredoxin and a reductase. It catalyzes the NADH-dependent oxidative demethylation of the broad leaf herbicide dicamba. DMO represents the first crystal structure of a Rieske non-heme iron oxygenase that performs an exocyclic monooxygenation, incorporating O(2) into a side-chain moiety and not a ring system. The structure reveals a 3-fold symmetric trimer (alpha(3)) in the crystallographic asymmetric unit with similar arrangement of neighboring inter-subunit Rieske domain and non-heme iron site enabling electron transport consistent with other structurally characterized Rieske oxygenases. While the Rieske domain is similar, differences are observed in the catalytic domain, which is smaller in sequence length than those described previously, yet possessing an active-site cavity of larger volume when compared to oxygenases with larger substrates. Consistent with the amphipathic substrate, the active site is designed to interact with both the carboxylate and aromatic ring with both key polar and hydrophobic interactions observed. DMO structures were solved with and without substrate (dicamba), product (3,6-dichlorosalicylic acid), and either cobalt or iron in the non-heme iron site. The substitution of cobalt for iron revealed an uncommon mode of non-heme iron binding trapped by the non-catalytic Co(2+), which, we postulate, may be transiently present in the native enzyme during the catalytic cycle. Thus, we present four DMO structures with resolutions ranging from 1.95 to 2.2 A, which, in sum, provide a snapshot of a dynamic enzyme where metal binding and substrate binding are coupled to observed structural changes in the non-heme iron and catalytic sites.

-	~~==About this Structure==~~	+	Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation.,D'Ordine RL, Rydel TJ, Storek MJ, Sturman EJ, Moshiri F, Bartlett RK, Brown GR, Eilers RJ, Dart C, Qi Y, Flasinski S, Franklin SJ J Mol Biol. 2009 Sep 18;392(2):481-97. Epub 2009 Jul 15. PMID:19616009<ref>PMID:19616009</ref>
-	~~[[3gb4]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3GB4 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:019616009</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Stenotrophomonas maltophilia]]		[[Category: Stenotrophomonas maltophilia]]
-	[[Category: Brown, G R.]]	+	[[Category: Brown, G R]]
-	[[Category: Moshiri, F.]]	+	[[Category: Moshiri, F]]
-	[[Category: Qi, Y.]]	+	[[Category: Qi, Y]]
-	[[Category: Rydel, T J.]]	+	[[Category: Rydel, T J]]
-	[[Category: Sturman, E J.]]	+	[[Category: Sturman, E J]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 09:15, 27 March 2013

OCA — Wed, 27 Mar 2013 09:15:03 GMT

←Older revision		Revision as of 09:15, 27 March 2013
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-	[[Image:3gb4.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gb4", 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_3gb4\| PDB=3gb4 \| SCENE= }}		{{STRUCTURE_3gb4\| PDB=3gb4 \| SCENE= }}
-
	===Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba===		===Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19616009}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19616009 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19616009}}		{{ABSTRACT_PUBMED_19616009}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:019616009</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019616009</ref><references group="xtra"/><references/>
	[[Category: Stenotrophomonas maltophilia]]		[[Category: Stenotrophomonas maltophilia]]
	[[Category: Brown, G R.]]		[[Category: Brown, G R.]]
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	[[Category: Rydel, T J.]]		[[Category: Rydel, T J.]]
	[[Category: Sturman, E J.]]		[[Category: Sturman, E J.]]
-	[[Category: 2fe-2]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron]]		[[Category: Iron]]

OCA: Protected "3gb4" [edit=sysop:move=sysop]

OCA — Thu, 26 May 2011 11:28:48 GMT

Protected "3gb4" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:28, 26 May 2011

OCA at 11:28, 26 May 2011

OCA — Thu, 26 May 2011 11:28:46 GMT

←Older revision		Revision as of 11:28, 26 May 2011
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-	{{Seed}}
	[[Image:3gb4.png\|left\|200px]]		[[Image:3gb4.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3GB4~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA].	+	[[3gb4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19616009~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019616009</ref><references group="xtra"/>
	[[Category: Stenotrophomonas maltophilia]]		[[Category: Stenotrophomonas maltophilia]]
	[[Category: Brown, G R.]]		[[Category: Brown, G R.]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rieske non-heme iron oxygenase]]		[[Category: Rieske non-heme iron oxygenase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 7 13:27:25 2009''

OCA at 11:27, 7 October 2009

OCA — Wed, 07 Oct 2009 11:27:26 GMT

←Older revision		Revision as of 11:27, 7 October 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3gb4.png\|left\|200px]]

-	The ~~entry 3gb4~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3gb4", 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_3gb4\| PDB=3gb4 \| SCENE= }}

-	~~Authors: Rydel, T.J., Sturman, E.J., Moshiri, F., Brown, G.R., Qi, Y.~~	+	===Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba===

-	Description: Dicamba Monooxygenase with Non-heme Cobalt and Dicamba

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May 20 16~~:34:46 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19616009}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19616009 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19616009}}
		+
		+	==About this Structure==
		+	3GB4 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GB4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19616009</ref><references group="xtra"/>
		+	[[Category: Stenotrophomonas maltophilia]]
		+	[[Category: Brown, G R.]]
		+	[[Category: Moshiri, F.]]
		+	[[Category: Qi, Y.]]
		+	[[Category: Rydel, T J.]]
		+	[[Category: Sturman, E J.]]
		+	[[Category: 2fe-2]]
		+	[[Category: Electron transport]]
		+	[[Category: Iron]]
		+	[[Category: Iron-sulfur]]
		+	[[Category: Metal-binding]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rieske non-heme iron oxygenase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 7 13:27:25 2009''

OCA at 13:34, 20 May 2009

OCA — Wed, 20 May 2009 13:34:47 GMT

←Older revision		Revision as of 13:34, 20 May 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3gb4 is ON HOLD	+	The entry 3gb4 is ON HOLD until Paper Publication

	Authors: Rydel, T.J., Sturman, E.J., Moshiri, F., Brown, G.R., Qi, Y.		Authors: Rydel, T.J., Sturman, E.J., Moshiri, F., Brown, G.R., Qi, Y.
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	Description: Dicamba Monooxygenase with Non-heme Cobalt and Dicamba		Description: Dicamba Monooxygenase with Non-heme Cobalt and Dicamba

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 14~~:46:15 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 16:34:46 2009''