5l1w - Revision history

OCA at 12:47, 4 October 2023

OCA — Wed, 04 Oct 2023 12:47:16 GMT

←Older revision		Revision as of 12:47, 4 October 2023
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	<StructureSection load='5l1w' size='340' side='right'caption='[[5l1w]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='5l1w' size='340' side='right'caption='[[5l1w]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l1w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~As_4.1610 As 4.1610~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l1w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_arenae Streptomyces arenae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L1W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=7PF:PENTALENOLACTONE+F'>7PF</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]] 2.06Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7PF:PENTALENOLACTONE+F'>7PF</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l1o\|5l1o]]~~, ~~[[5l1p\|5l1p]], [[5l1q\|5l1q]], [[5l1r\|5l1r]], [[5l1s\|5l1s]], [[5l1t\|5l1t]], [[5l1u\|5l1u]], [[5l1v\|5l1v]]~~<~~/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=5l1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1w OCA], [https://pdbe.org/5l1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l1w RCSB], [https://www.ebi.ac.uk/pdbsum/5l1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1w ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">pntM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29301 AS 4.1610])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenolactone_synthase Pentalenolactone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.19.8 1.14.19.8] </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=5l1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1w OCA], [~~http~~://pdbe.org/5l1w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l1w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l1w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1w ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PNTM_STRAE PNTM_STRAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1610]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pentalenolactone synthase~~]]	+	[[Category: Streptomyces arenae]]
-	[[Category: Cane~~, D E~~]]	+	[[Category: Cane DE]]
-	[[Category: Duan, L]]	+	[[Category: Duan L]]
-	[[Category: Jogl, G]]	+	[[Category: Jogl G]]
-	~~[[Category: 2-mercaptoethanol]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: M81c]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pentalenolactone f]]~~	+
-	~~[[Category: Pntm~~]]	+

OCA at 06:40, 5 August 2020

OCA — Wed, 05 Aug 2020 06:40:26 GMT

←Older revision		Revision as of 06:40, 5 August 2020
Line 1:		Line 1:

	==X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 PntM with pentalenolactone F==		==X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 PntM with pentalenolactone F==
-	<StructureSection load='5l1w' size='340' side='right' caption='[[5l1w]], [[Resolution\|resolution]] 2.06Å' scene=''>	+	<StructureSection load='5l1w' size='340' side='right'caption='[[5l1w]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l1w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l1w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1610 As 4.1610]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L1W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7PF:PENTALENOLACTONE+F'>7PF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7PF:PENTALENOLACTONE+F'>7PF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l1o\|5l1o]], [[5l1p\|5l1p]], [[5l1q\|5l1q]], [[5l1r\|5l1r]], [[5l1s\|5l1s]], [[5l1t\|5l1t]], [[5l1u\|5l1u]], [[5l1v\|5l1v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l1o\|5l1o]], [[5l1p\|5l1p]], [[5l1q\|5l1q]], [[5l1r\|5l1r]], [[5l1s\|5l1s]], [[5l1t\|5l1t]], [[5l1u\|5l1u]], [[5l1v\|5l1v]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pntM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29301 AS 4.1610])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenolactone_synthase Pentalenolactone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.19.8 1.14.19.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenolactone_synthase Pentalenolactone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.19.8 1.14.19.8] </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=5l1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1w OCA], [http://pdbe.org/5l1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l1w RCSB], [http://www.ebi.ac.uk/pdbsum/5l1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1w 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=5l1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1w OCA], [http://pdbe.org/5l1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l1w RCSB], [http://www.ebi.ac.uk/pdbsum/5l1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1w ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: As 4 1610]]
		+	[[Category: Large Structures]]
	[[Category: Pentalenolactone synthase]]		[[Category: Pentalenolactone synthase]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]

OCA at 15:13, 14 September 2016

OCA — Wed, 14 Sep 2016 15:13:15 GMT

←Older revision		Revision as of 15:13, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5l1w is ~~ON HOLD~~	+	==X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 PntM with pentalenolactone F==
		+	<StructureSection load='5l1w' size='340' side='right' caption='[[5l1w]], [[Resolution\|resolution]] 2.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5l1w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L1W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7PF:PENTALENOLACTONE+F'>7PF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l1o\|5l1o]], [[5l1p\|5l1p]], [[5l1q\|5l1q]], [[5l1r\|5l1r]], [[5l1s\|5l1s]], [[5l1t\|5l1t]], [[5l1u\|5l1u]], [[5l1v\|5l1v]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenolactone_synthase Pentalenolactone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.19.8 1.14.19.8] </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=5l1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1w OCA], [http://pdbe.org/5l1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l1w RCSB], [http://www.ebi.ac.uk/pdbsum/5l1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1w ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The final step in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone (1) is the highly unusual cytochrome P450-catalyzed, oxidative rearrangement of pentalenolactone F (2), involving the transient generation and rearrangement of a neopentyl cation. In Streptomyces arenae this reaction is catalyzed by CYP161C2 (PntM), with highly conserved orthologues being present in the pentalenolactone biosynthetic gene clusters of at least 10 other Actinomycetes. The 2.00 - 2.28 A crystal structures of substrate-free PntM, as well as PntM with bound substrate 2, product 1, and substrate analogue 6,7-dihydropentalenolactone F (7) have revealed the close interaction of bound ligand with three active site residues, F232, M77, and M81 that are unique to PntM and its orthologues and absent from essentially all other P450s. Site-directed mutagenesis, ligand-binding measurements, steady-state kinetics, and reaction product profiles have established there is no special stabilization of reactive cationic intermediates by any of these side chains. Reduced substrate analogue 7 did not undergo either oxidative rearrangement or simple hydroxylation, suggesting that the C1 carbocation is not anchimerically stabilized by the 6,7-double bond of 2. The crystal structures also revealed plausible proton relay networks likely involved in the generation of the key characteristic P450 oxidizing species, Compound I, and in mediating stereospecific deprotonation of H-3re of the substrate. We conclude that the unusual carbocation intermediate results from outer shell electron transfer from the transiently generated C1 radical to the tightly paired heme- *Fe3+-OH radical species. The oxidative electron transfer is kinetically dominant as a result of the unusually strong steric barrier to oxygen rebound to the neopentyl center C-1si which is flanked on each neighboring carbon by syn-axial substituents.

-	~~Authors~~: Duan, L., Jogl, G., Cane~~, D~~.E.	+	The Cytochrome P450-Catalyzed Oxidative Rearrangement in the Final Step of Pentalenolactone Biosynthesis: Substrate Structure Determines Mechanism.,Duan L, Jogl G, Cane DE J Am Chem Soc. 2016 Sep 2. PMID:27588339<ref>PMID:27588339</ref>

-	~~Description: X-ray Structure~~ of ~~2-Mercaptoethanol modified M81C mutant~~ of ~~Cytochrome P450 PntM with pentalenolactone F~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Jogl~~, G]]	+	<div class="pdbe-citations 5l1w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pentalenolactone synthase]]
		+	[[Category: Cane, D E]]
	[[Category: Duan, L]]		[[Category: Duan, L]]
-	[[Category: ~~Cane~~, ~~D.E~~]]	+	[[Category: Jogl, G]]
		+	[[Category: 2-mercaptoethanol]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: M81c]]
		+	[[Category: Mutant]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pentalenolactone f]]
		+	[[Category: Pntm]]

OCA: Protected "5l1w" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2016 14:00:12 GMT

Protected "5l1w" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:00, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5l1w is ON HOLD Authors: Duan, L., Jogl, G., Cane, D.E. Description: X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 P...

OCA — Wed, 10 Aug 2016 14:00:11 GMT

New page: '''Unreleased structure''' The entry 5l1w is ON HOLD Authors: Duan, L., Jogl, G., Cane, D.E. Description: X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 P...

New page

'''Unreleased structure'''

The entry 5l1w is ON HOLD

Authors: Duan, L., Jogl, G., Cane, D.E.

Description: X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 PntM with pentalenolactone F
[[Category: Unreleased Structures]]
[[Category: Jogl, G]]
[[Category: Duan, L]]
[[Category: Cane, D.E]]