6vsh - Revision history

OCA at 08:18, 11 October 2023

OCA — Wed, 11 Oct 2023 08:18:37 GMT

←Older revision		Revision as of 08:18, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6vsh' size='340' side='right'caption='[[6vsh]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6vsh' size='340' side='right'caption='[[6vsh]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vsh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VSH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6VSH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vsh]] 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=6VSH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VSH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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]] 3Å</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=6vsh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vsh OCA], [~~http~~://pdbe.org/6vsh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vsh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vsh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vsh ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></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=6vsh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vsh OCA], [https://pdbe.org/6vsh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vsh RCSB], [https://www.ebi.ac.uk/pdbsum/6vsh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vsh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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>	+	[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rydel, T J~~]]	+	[[Category: Stenotrophomonas maltophilia]]
-	[[Category: ~~Electron transport]]~~	+	[[Category: Rydel TJ]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:29, 26 February 2020

OCA — Wed, 26 Feb 2020 09:29:03 GMT

←Older revision		Revision as of 09:29, 26 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vsh is ~~ON HOLD~~	+	==Crystal structure of apo Dicamba Monooxygenase==
		+	<StructureSection load='6vsh' size='340' side='right'caption='[[6vsh]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6vsh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VSH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VSH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></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=6vsh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vsh OCA], [http://pdbe.org/6vsh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vsh RCSB], [http://www.ebi.ac.uk/pdbsum/6vsh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vsh ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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>
		+	<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.

-	~~Authors~~: Rydel, T.J.	+	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>

-	~~Description: Crystal structure~~ of ~~apo Dicamba Monooxygenase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Rydel, T.J]]	+	<div class="pdbe-citations 6vsh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rydel, T J]]
		+	[[Category: Electron transport]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 19 Feb 2020 05:20:28 GMT

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

←Older revision

Revision as of 05:20, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vsh is ON HOLD Authors: Rydel, T.J. Description: Crystal structure of apo Dicamba Monooxygenase Category: Unreleased Structures [[Category: Ry...

OCA — Wed, 19 Feb 2020 05:20:26 GMT

New page: '''Unreleased structure''' The entry 6vsh is ON HOLD Authors: Rydel, T.J. Description: Crystal structure of apo Dicamba Monooxygenase Category: Unreleased Structures [[Category: Ry...

New page

'''Unreleased structure'''

The entry 6vsh is ON HOLD

Authors: Rydel, T.J.

Description: Crystal structure of apo Dicamba Monooxygenase
[[Category: Unreleased Structures]]
[[Category: Rydel, T.J]]