6zi3 - Revision history

OCA at 11:52, 1 February 2024

OCA — Thu, 01 Feb 2024 11:52:42 GMT

←Older revision		Revision as of 11:52, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='6zi3' size='340' side='right'caption='[[6zi3]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='6zi3' size='340' side='right'caption='[[6zi3]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zi3]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_antibioticus"_waksman_and_woodruff_1941 "actinomyces~~ antibioticus~~" waksman and woodruff 1941~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZI3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZI3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zi3]] 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=6ZI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZI3 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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.08Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6zhz\|6zhz]], [[6zi2\|6zi2]]</div></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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oleP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1890 "Actinomyces antibioticus" Waksman and Woodruff 1941])</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=6zi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi3 OCA], [https://pdbe.org/6zi3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zi3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zi3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi3 ProSAT]</span></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=6zi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi3 OCA], [~~http~~://pdbe.org/6zi3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zi3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zi3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi3 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 ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6zi3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6zi3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Actinomyces antibioticus waksman and woodruff 1941]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Freda, I]]	+	[[Category: Streptomyces antibioticus]]
-	[[Category: Montemiglio~~, L C~~]]	+	[[Category: Freda I]]
-	[[Category: Parisi, G]]	+	[[Category: Montemiglio LC]]
-	[[Category: Savino, C]]	+	[[Category: Parisi G]]
-	[[Category: Vallone, B]]	+	[[Category: Savino C]]
-	~~[[Category: 8a-deoxyoleandolide]]~~	+	[[Category: Vallone B]]
-	~~[[Category: 8a-deoxyoleandolide monooxygenase]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:01, 24 December 2020

OCA — Thu, 24 Dec 2020 11:01:24 GMT

←Older revision		Revision as of 11:01, 24 December 2020
Line 1:		Line 1:

	==Crystal structure of OleP-6DEB bound to L-rhamnose==		==Crystal structure of OleP-6DEB bound to L-rhamnose==
-	<StructureSection load='6zi3' size='340' side='right'caption='[[6zi3]]' scene=''>	+	<StructureSection load='6zi3' size='340' side='right'caption='[[6zi3]], [[Resolution\|resolution]] 2.08Å' 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=6ZI3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZI3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zi3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_antibioticus"_waksman_and_woodruff_1941 "actinomyces antibioticus" waksman and woodruff 1941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZI3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZI3 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=6zi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi3 OCA], [http://pdbe.org/6zi3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zi3 RCSB], [http://www.ebi.ac.uk/pdbsum/6zi3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi3 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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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;'>[[6zhz\|6zhz]], [[6zi2\|6zi2]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oleP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1890 "Actinomyces antibioticus" Waksman and Woodruff 1941])</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=6zi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi3 OCA], [http://pdbe.org/6zi3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zi3 RCSB], [http://www.ebi.ac.uk/pdbsum/6zi3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi3 ProSAT]</span></td></tr>
	</table>		</table>
		+	<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 6zi3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Actinomyces antibioticus waksman and woodruff 1941]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Freda I]]	+	[[Category: Freda, I]]
-	[[Category: Montemiglio LC]]	+	[[Category: Montemiglio, L C]]
-	[[Category: Parisi G]]	+	[[Category: Parisi, G]]
-	[[Category: Savino C]]	+	[[Category: Savino, C]]
-	[[Category: Vallone B]]	+	[[Category: Vallone, B]]
		+	[[Category: 8a-deoxyoleandolide]]
		+	[[Category: 8a-deoxyoleandolide monooxygenase]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Oxidoreductase]]

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
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zi3 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of OleP-6DEB bound to L-rhamnose==
-		+	<StructureSection load='6zi3' size='340' side='right'caption='[[6zi3]]' 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=6ZI3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZI3 FirstGlance]. <br>
-	~~Description: Crystal structure of OleP-6DEB 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=6zi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zi3 OCA], [http://pdbe.org/6zi3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zi3 RCSB], [http://www.ebi.ac.uk/pdbsum/6zi3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zi3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Savino, C~~]]	+	__TOC__
-	[[Category: ~~Vallone, B~~]]	+	</StructureSection>
-	[[Category: Parisi, G]]	+	[[Category: Large Structures]]
-	[[Category: ~~Freda, I~~]]	+	[[Category: Freda I]]
-	[[Category: ~~Montemiglio, L.C~~]]	+	[[Category: Montemiglio LC]]
		+	[[Category: Parisi G]]
		+	[[Category: Savino C]]
		+	[[Category: Vallone B]]

OCA at 03:54, 5 August 2020

OCA — Wed, 05 Aug 2020 03:54:13 GMT

←Older revision		Revision as of 03:54, 5 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6zi3 is ON HOLD	+	The entry 6zi3 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.
Line 7:		Line 7:
	Description: Crystal structure of OleP-6DEB bound to L-rhamnose		Description: Crystal structure of OleP-6DEB bound to L-rhamnose
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Montemiglio, L.C]]
	[[Category: Savino, C]]		[[Category: Savino, C]]
	[[Category: Vallone, B]]		[[Category: Vallone, B]]
	[[Category: Parisi, G]]		[[Category: Parisi, G]]
	[[Category: Freda, I]]		[[Category: Freda, I]]
		+	[[Category: Montemiglio, L.C]]

OCA: Protected "6zi3" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2020 11:10:36 GMT

Protected "6zi3" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:10, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zi3 is ON HOLD Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I. Description: Crystal structure of OleP-6DEB bound to L-r...

OCA — Wed, 08 Jul 2020 11:10:35 GMT

New page: '''Unreleased structure''' The entry 6zi3 is ON HOLD Authors: Montemiglio, L.C., Savino, C., Vallone, B., Parisi, G., Freda, I. Description: Crystal structure of OleP-6DEB bound to L-r...

New page

'''Unreleased structure'''

The entry 6zi3 is ON HOLD

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

Description: Crystal structure of OleP-6DEB bound to L-rhamnose
[[Category: Unreleased Structures]]
[[Category: Montemiglio, L.C]]
[[Category: Savino, C]]
[[Category: Vallone, B]]
[[Category: Parisi, G]]
[[Category: Freda, I]]