6zi7 - Revision history

OCA at 11:52, 1 February 2024

OCA — Thu, 01 Feb 2024 11:52:47 GMT

←Older revision		Revision as of 11:52, 1 February 2024
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	==Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose==		==Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose==
-	<StructureSection load='6zi7' size='340' side='right'caption='[[6zi7]]' scene=''>	+	<StructureSection load='6zi7' size='340' side='right'caption='[[6zi7]], [[Resolution\|resolution]] 2.28Å' 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=6ZI7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZI7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zi7]] 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=6ZI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZI7 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6zi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi7 OCA], [~~http~~://pdbe.org/6zi7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zi7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zi7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi7 ProSAT]</span></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]] 2.28Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=QR8:(3~{R},4~{S},5~{R},6~{S},7~{S},9~{S},11~{R},12~{S},13~{R},14~{R})-3,5,7,9,11,13,14-heptamethyl-4,6,12-tris(oxidanyl)-1-oxacyclotetradecane-2,10-dione'>QR8</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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=6zi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi7 OCA], [https://pdbe.org/6zi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zi7 RCSB], [https://www.ebi.ac.uk/pdbsum/6zi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q59819_STRAT Q59819_STRAT]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cytochrome P450 OleP catalyzes the epoxidation of aliphatic carbons on both the aglycone 8.8a-deoxyoleandolide (DEO) and the monoglycosylated L-olivosyl-8.8a-deoxyoleandolide (L-O-DEO) intermediates of oleandomycin biosynthesis. We investigated the substrate versatility of the enzyme. X-ray and equilibrium binding data show that the aglycone DEO loosely fits the OleP active site, triggering the closure that prepares it for catalysis only on a minor population of enzyme. The open-to-closed state transition allows solvent molecules to accumulate in a cavity that forms upon closure, mediating protein-substrate interactions. In silico docking of the monoglycosylated L-O-DEO in the closed OleP-DEO structure shows that the L-olivosyl moiety can be hosted in the same cavity, replacing solvent molecules and directly contacting structural elements involved in the transition. X-ray structures of aglycone-bound OleP in the presence of L-rhamnose confirm the cavity as a potential site for sugar binding. All considered, we propose L-O-DEO as the optimal substrate of OleP, the L-olivosyl moiety possibly representing the molecular wedge that triggers a more efficient structural response upon substrate binding, favoring and stabilizing the enzyme closure before catalysis. OleP substrate versatility is supported by structural solvent molecules that compensate for the absence of a glycosyl unit when the aglycone is bound.
		+
		+	Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate.,Parisi G, Freda I, Exertier C, Cecchetti C, Gugole E, Cerutti G, D'Auria L, Macone A, Vallone B, Savino C, Montemiglio LC Biomolecules. 2020 Oct 6;10(10). pii: biom10101411. doi: 10.3390/biom10101411. PMID:33036250<ref>PMID:33036250</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zi7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Streptomyces antibioticus]]
	[[Category: Freda I]]		[[Category: Freda I]]
	[[Category: Montemiglio LC]]		[[Category: Montemiglio LC]]

OCA at 08:16, 21 October 2020

OCA — Wed, 21 Oct 2020 08:16:08 GMT

←Older revision		Revision as of 08:16, 21 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6zi7 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose==
-		+	<StructureSection load='6zi7' size='340' side='right'caption='[[6zi7]]' scene=''>
-	~~Authors~~: ~~Montemiglio, L~~.C., ~~Savino~~, C., ~~Vallone, B~~., ~~Parisi, G~~., ~~Freda, I~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZI7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZI7 FirstGlance]. <br>
-	~~Description: Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi7 OCA], [http://pdbe.org/6zi7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zi7 RCSB], [http://www.ebi.ac.uk/pdbsum/6zi7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi7 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Montemiglio, L.C~~]]	+	__TOC__
-	[[Category: ~~Savino, C~~]]	+	</StructureSection>
-	[[Category: ~~Vallone, B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Parisi, G~~]]	+	[[Category: Freda I]]
-	[[Category: ~~Freda, I~~]]	+	[[Category: Montemiglio LC]]
		+	[[Category: Parisi G]]
		+	[[Category: Savino C]]
		+	[[Category: Vallone B]]

OCA at 08:10, 12 August 2020

OCA — Wed, 12 Aug 2020 08:10:33 GMT

←Older revision		Revision as of 08:10, 12 August 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6zi7 is ON HOLD	+	The entry 6zi7 is ON HOLD until Paper Publication

	Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I.		Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I.

OCA: Protected "6zi7" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2020 11:10:49 GMT

Protected "6zi7" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:10, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zi7 is ON HOLD Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I. Description: Crystal structure of OleP-oleandolide(DEO) ...

OCA — Wed, 08 Jul 2020 11:10:48 GMT

New page: '''Unreleased structure''' The entry 6zi7 is ON HOLD Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I. Description: Crystal structure of OleP-oleandolide(DEO) ...

New page

'''Unreleased structure'''

The entry 6zi7 is ON HOLD

Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I.

Description: Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose
[[Category: Unreleased Structures]]
[[Category: Montemiglio, L.C]]
[[Category: Savino, C]]
[[Category: Vallone, B]]
[[Category: Parisi, G]]
[[Category: Freda, I]]