7q6r - Revision history

OCA at 13:14, 1 February 2024

OCA — Thu, 01 Feb 2024 13:14:39 GMT

←Older revision		Revision as of 13:14, 1 February 2024
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	<StructureSection load='7q6r' size='340' side='right'caption='[[7q6r]], [[Resolution\|resolution]] 2.44Å' scene=''>		<StructureSection load='7q6r' size='340' side='right'caption='[[7q6r]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7q6r]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7q6r]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q6R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DEB:6-DEOXYERYTHRONOLIDE+B'>DEB</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.44Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DEB:6-DEOXYERYTHRONOLIDE+B'>DEB</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=7q6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q6r OCA], [https://pdbe.org/7q6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q6r RCSB], [https://www.ebi.ac.uk/pdbsum/7q6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q6r 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=7q6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q6r OCA], [https://pdbe.org/7q6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q6r RCSB], [https://www.ebi.ac.uk/pdbsum/7q6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q6r ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q59819_STRAT Q59819_STRAT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7q6r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7q6r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Exertier, C]]	+	[[Category: Streptomyces antibioticus]]
-	[[Category: Freda, I]]	+	[[Category: Exertier C]]
-	[[Category: Gugole, E]]	+	[[Category: Freda I]]
-	[[Category: Montemiglio~~, L C~~]]	+	[[Category: Gugole E]]
-	[[Category: Savino, C]]	+	[[Category: Montemiglio LC]]
-	[[Category: Vallone, B]]	+	[[Category: Savino C]]
-	~~[[Category: Cytochrome p450]]~~	+	[[Category: Vallone B]]
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oleandomicine]]~~	+
-	~~[[Category: Olep]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:36, 9 February 2022

OCA — Wed, 09 Feb 2022 07:36:36 GMT

←Older revision		Revision as of 07:36, 9 February 2022
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	==OleP mutant E89Y in complex with 6DEB==		==OleP mutant E89Y in complex with 6DEB==
-	<StructureSection load='7q6r' size='340' side='right'caption='[[7q6r]]' scene=''>	+	<StructureSection load='7q6r' size='340' side='right'caption='[[7q6r]], [[Resolution\|resolution]] 2.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7q6r]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q6R FirstGlance]. <br>
-	</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=7q6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q6r OCA], [https://pdbe.org/7q6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q6r RCSB], [https://www.ebi.ac.uk/pdbsum/7q6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q6r ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DEB:6-DEOXYERYTHRONOLIDE+B'>DEB</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=7q6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q6r OCA], [https://pdbe.org/7q6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q6r RCSB], [https://www.ebi.ac.uk/pdbsum/7q6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q6r ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Substrate binding to the cytochrome P450 OleP is coupled to a large open-to-closed transition that remodels the active site, minimizing its exposure to the external solvent. When the aglycone substrate binds, a small empty cavity is formed between the I and G helices, the BC loop, and the substrate itself, where solvent molecules accumulate mediating substrate-enzyme interactions. Herein, we analyzed the role of this cavity in substrate binding to OleP by producing three mutants (E89Y, G92W, and S240Y) to decrease its volume. The crystal structures of the OleP mutants in the closed state bound to the aglycone 6DEB showed that G92W and S240Y occupied the cavity, providing additional contact points with the substrate. Conversely, mutation E89Y induces a flipped-out conformation of this amino acid side chain, that points towards the bulk, increasing the empty volume. Equilibrium titrations and molecular dynamic simulations indicate that the presence of a bulky residue within the cavity impacts the binding properties of the enzyme, perturbing the conformational space explored by the complexes. Our data highlight the relevance of this region in OleP substrate binding and suggest that it represents a key substrate-protein contact site to consider in the perspective of redirecting its activity towards alternative compounds.
		+
		+	Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics.,Montemiglio LC, Gugole E, Freda I, Exertier C, D'Auria L, Chen CG, Nardi AN, Cerutti G, Parisi G, D'Abramo M, Savino C, Vallone B Biomolecules. 2021 Dec 31;12(1). pii: biom12010055. doi: 10.3390/biom12010055. PMID:35053203<ref>PMID:35053203</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7q6r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Exertier C]]	+	[[Category: Exertier, C]]
-	[[Category: Freda I]]	+	[[Category: Freda, I]]
-	[[Category: Gugole E]]	+	[[Category: Gugole, E]]
-	[[Category: Montemiglio LC]]	+	[[Category: Montemiglio, L C]]
-	[[Category: Savino C]]	+	[[Category: Savino, C]]
-	[[Category: Vallone B]]	+	[[Category: Vallone, B]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Mutant]]
		+	[[Category: Oleandomicine]]
		+	[[Category: Olep]]
		+	[[Category: Oxidoreductase]]

OCA at 07:02, 27 January 2022

OCA — Thu, 27 Jan 2022 07:02:46 GMT

←Older revision		Revision as of 07:02, 27 January 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7q6r ~~is ON HOLD until Paper Publication~~	+	==OleP mutant E89Y in complex with 6DEB==
-		+	<StructureSection load='7q6r' size='340' side='right'caption='[[7q6r]]' scene=''>
-	~~Authors~~: ~~Savino, C~~., ~~Montemiglio, L~~.C.~~, Vallone, B~~., ~~Exertier, C~~., ~~Freda~~, I., ~~Gugole, E~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q6R FirstGlance]. <br>
-	~~Description: OleP mutant E89Y in complex with 6DEB~~	+	</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=7q6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q6r OCA], [https://pdbe.org/7q6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q6r RCSB], [https://www.ebi.ac.uk/pdbsum/7q6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q6r ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Savino,~~ C]]	+	__TOC__
-	[[Category: ~~Vallone, B~~]]	+	</StructureSection>
-	[[Category: ~~Freda, I~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Gugole, E~~]]	+	[[Category: Exertier C]]
-	[[Category: ~~Exertier,~~ C]]	+	[[Category: Freda I]]
-	[[Category: ~~Montemiglio, L.C~~]]	+	[[Category: Gugole E]]
		+	[[Category: Montemiglio LC]]
		+	[[Category: Savino C]]
		+	[[Category: Vallone B]]

OCA at 05:02, 1 December 2021

OCA — Wed, 01 Dec 2021 05:02:59 GMT

←Older revision		Revision as of 05:02, 1 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7q6r is ON HOLD	+	The entry 7q6r is ON HOLD until Paper Publication

	Authors: Savino, C., Montemiglio, L.C., Vallone, B., Exertier, C., Freda, I., Gugole, E.		Authors: Savino, C., Montemiglio, L.C., Vallone, B., Exertier, C., Freda, I., Gugole, E.
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	Description: OleP mutant E89Y in complex with 6DEB		Description: OleP mutant E89Y in complex with 6DEB
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Gugole, E]]
-	[[Category: Montemiglio, L.C]]
	[[Category: Savino, C]]		[[Category: Savino, C]]
	[[Category: Vallone, B]]		[[Category: Vallone, B]]
	[[Category: Freda, I]]		[[Category: Freda, I]]
		+	[[Category: Gugole, E]]
	[[Category: Exertier, C]]		[[Category: Exertier, C]]
		+	[[Category: Montemiglio, L.C]]

OCA: Protected "7q6r" [edit=sysop:move=sysop]

OCA — Wed, 17 Nov 2021 12:04:27 GMT

Protected "7q6r" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:04, 17 November 2021

OCA: New page: '''Unreleased structure''' The entry 7q6r is ON HOLD Authors: Savino, C., Montemiglio, L.C., Vallone, B., Exertier, C., Freda, I., Gugole, E. Description: OleP mutant E89Y in complex w...

OCA — Wed, 17 Nov 2021 12:04:26 GMT

New page: '''Unreleased structure''' The entry 7q6r is ON HOLD Authors: Savino, C., Montemiglio, L.C., Vallone, B., Exertier, C., Freda, I., Gugole, E. Description: OleP mutant E89Y in complex w...

New page

'''Unreleased structure'''

The entry 7q6r is ON HOLD

Authors: Savino, C., Montemiglio, L.C., Vallone, B., Exertier, C., Freda, I., Gugole, E.

Description: OleP mutant E89Y in complex with 6DEB
[[Category: Unreleased Structures]]
[[Category: Gugole, E]]
[[Category: Montemiglio, L.C]]
[[Category: Savino, C]]
[[Category: Vallone, B]]
[[Category: Freda, I]]
[[Category: Exertier, C]]