6m4p - Revision history

OCA at 15:15, 29 November 2023

2023-11-29T15:15:22Z

←Older revision		Revision as of 15:15, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='6m4p' size='340' side='right'caption='[[6m4p]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6m4p' size='340' side='right'caption='[[6m4p]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m4p]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_27465 Atcc 27465~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M4P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m4p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_spectabilis Streptomyces spectabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M4P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=F4O:6~~-~~methoxy-streptovaricin+C'>F4O</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~stvP2 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=68270 ATCC 27465])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F4O:6-methoxy-streptovaricin+C'>F4O</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6m4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4p OCA], [~~http~~://pdbe.org/6m4p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m4p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m4p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4p 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=6m4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4p OCA], [https://pdbe.org/6m4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m4p RCSB], [https://www.ebi.ac.uk/pdbsum/6m4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A286SBY7_STRST A0A286SBY7_STRST]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6m4p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6m4p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 27465]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, X]]	+	[[Category: Streptomyces spectabilis]]
-	[[Category: Deng, Z]]	+	[[Category: Chen X]]
-	[[Category: Hu, C]]	+	[[Category: Deng Z]]
-	[[Category: Li, Z]]	+	[[Category: Hu C]]
-	[[Category: Liu, Y]]	+	[[Category: Li Z]]
-	[[Category: Luo, M]]	+	[[Category: Liu Y]]
-	[[Category: Mei, Q]]	+	[[Category: Luo M]]
-	[[Category: Sun, G]]	+	[[Category: Mei Q]]
-	[[Category: Sun, Y]]	+	[[Category: Sun G]]
-	[[Category: Zhang, Z]]	+	[[Category: Sun Y]]
-	~~[[Category: Antibiotic]]~~	+	[[Category: Zhang Z]]
-	~~[[Category: P450 anti-mrsa streptovaricin c methylenedioxy bridge stvp2 substrate-bound structure~~]]	+

OCA at 11:23, 23 September 2020

2020-09-23T11:23:17Z

←Older revision		Revision as of 11:23, 23 September 2020
Line 1:		Line 1:

	==Cytochrome P450 monooxygenase StvP2 substrate-bound structure==		==Cytochrome P450 monooxygenase StvP2 substrate-bound structure==
-	<StructureSection load='6m4p' size='340' side='right'caption='[[6m4p]]' scene=''>	+	<StructureSection load='6m4p' size='340' side='right'caption='[[6m4p]], [[Resolution\|resolution]] 2.30Å' 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=6M4P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M4P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m4p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_27465 Atcc 27465]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M4P 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=6m4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4p OCA], [http://pdbe.org/6m4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m4p RCSB], [http://www.ebi.ac.uk/pdbsum/6m4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4p 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=F4O:6-methoxy-streptovaricin+C'>F4O</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">stvP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=68270 ATCC 27465])</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=6m4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4p OCA], [http://pdbe.org/6m4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m4p RCSB], [http://www.ebi.ac.uk/pdbsum/6m4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Streptovaricin C is a naphthalenic ansamycin antibiotic structurally similar to rifamycins with potential anti-MRSA bioactivities. However, the formation mechanism of the most fascinating and bioactivity-related methylenedioxy bridge (MDB) moiety in streptovaricins is unclear. Based on genetic and biochemical evidences, we herein clarify that the P450 enzyme StvP2 catalyzes the MDB formation in streptovaricins, with an atypical substrate inhibition kinetics. Furthermore, X-ray crystal structures in complex with substrate and structure-based mutagenesis reveal the intrinsic details of the enzymatic reaction. The mechanism of MDB formation is proposed to be an intramolecular nucleophilic substitution resulting from the hydroxylation by the heme core and the keto-enol tautomerization via a crucial catalytic triad (Asp89-His92-Arg72) in StvP2. In addition, in vitro reconstitution uncovers that C6-O-methylation and C4-O-acetylation of streptovaricins are necessary prerequisites for the MDB formation. This work provides insight for the MDB formation and adds evidence in support of the functional versatility of P450 enzymes.
		+
		+	Uncovering the cytochrome P450-catalyzed methylenedioxy bridge formation in streptovaricins biosynthesis.,Sun G, Hu C, Mei Q, Luo M, Chen X, Li Z, Liu Y, Deng Z, Zhang Z, Sun Y Nat Commun. 2020 Sep 9;11(1):4501. doi: 10.1038/s41467-020-18336-5. PMID:32908132<ref>PMID:32908132</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6m4p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 27465]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen X]]	+	[[Category: Chen, X]]
-	[[Category: Deng Z]]	+	[[Category: Deng, Z]]
-	[[Category: Hu C]]	+	[[Category: Hu, C]]
-	[[Category: Li Z]]	+	[[Category: Li, Z]]
-	[[Category: Liu Y]]	+	[[Category: Liu, Y]]
-	[[Category: Luo M]]	+	[[Category: Luo, M]]
-	[[Category: Mei Q]]	+	[[Category: Mei, Q]]
-	[[Category: Sun G]]	+	[[Category: Sun, G]]
-	[[Category: Sun Y]]	+	[[Category: Sun, Y]]
-	[[Category: Zhang Z]]	+	[[Category: Zhang, Z]]
		+	[[Category: Antibiotic]]
		+	[[Category: P450 anti-mrsa streptovaricin c methylenedioxy bridge stvp2 substrate-bound structure]]

OCA at 09:45, 12 August 2020

2020-08-12T09:45:25Z

←Older revision		Revision as of 09:45, 12 August 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6m4p ~~is ON HOLD until Paper Publication~~	+	==Cytochrome P450 monooxygenase StvP2 substrate-bound structure==
-		+	<StructureSection load='6m4p' size='340' side='right'caption='[[6m4p]]' scene=''>
-	~~Authors~~: ~~Sun, G~~.~~, Hu, C~~.~~, Mei, Q~~.~~, Luo, M~~.~~, Chen, X~~., ~~Li, Z~~., ~~Liu, Y~~., ~~Deng, Z~~., ~~Zhang, Z~~., ~~Sun, Y~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M4P FirstGlance]. <br>
-	~~Description: Cytochrome P450 monooxygenase StvP2 substrate-bound structure~~	+	</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=6m4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4p OCA], [http://pdbe.org/6m4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m4p RCSB], [http://www.ebi.ac.uk/pdbsum/6m4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4p ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Li, Z~~]]	+	__TOC__
-	[[Category: ~~Zhang,~~ Z]]	+	</StructureSection>
-	[[Category: ~~Chen, X~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mei, Q~~]]	+	[[Category: Chen X]]
-	[[Category: ~~Sun, G~~]]	+	[[Category: Deng Z]]
-	[[Category: ~~Liu, Y~~]]	+	[[Category: Hu C]]
-	[[Category: ~~Luo, M~~]]	+	[[Category: Li Z]]
-	[[Category: Sun~~, Y~~]]	+	[[Category: Liu Y]]
-	[[Category: ~~Deng, Z~~]]	+	[[Category: Luo M]]
-	[[Category: ~~Hu, C~~]]	+	[[Category: Mei Q]]
		+	[[Category: Sun G]]
		+	[[Category: Sun Y]]
		+	[[Category: Zhang Z]]

OCA at 04:08, 22 April 2020

2020-04-22T04:08:48Z

←Older revision		Revision as of 04:08, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6m4p is ON HOLD	+	The entry 6m4p is ON HOLD until Paper Publication

	Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y.		Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y.

-	Description: ~~Uncovering the~~ P450~~-catalyzed Methylenedioxy Bridge Formation in Streptovaricins Biosynthesis~~ StvP2 substrate-bound structure	+	Description: Cytochrome P450 monooxygenase StvP2 substrate-bound structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Li, Z]]
	[[Category: Zhang, Z]]		[[Category: Zhang, Z]]
	[[Category: Chen, X]]		[[Category: Chen, X]]
	[[Category: Mei, Q]]		[[Category: Mei, Q]]
	[[Category: Sun, G]]		[[Category: Sun, G]]
-	[[Category: Luo, M]]
-	[[Category: Li, Z]]
	[[Category: Liu, Y]]		[[Category: Liu, Y]]
		+	[[Category: Luo, M]]
	[[Category: Sun, Y]]		[[Category: Sun, Y]]
	[[Category: Deng, Z]]		[[Category: Deng, Z]]
	[[Category: Hu, C]]		[[Category: Hu, C]]

OCA at 08:15, 27 March 2020

2020-03-27T08:15:19Z

←Older revision		Revision as of 08:15, 27 March 2020
Line 5:		Line 5:
	Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y.		Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y.

-	Description: Uncovering the ~~Biosynthetic Pathway of the~~ Methylenedioxy Bridge in Streptovaricins~~: from Damavaricin C to Streptovaricin C by Cytochrome P450 Monooxygenases~~	+	Description: Uncovering the P450-catalyzed Methylenedioxy Bridge Formation in Streptovaricins Biosynthesis StvP2 substrate-bound structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Li, Z]]
	[[Category: Zhang, Z]]		[[Category: Zhang, Z]]
	[[Category: Chen, X]]		[[Category: Chen, X]]
	[[Category: Mei, Q]]		[[Category: Mei, Q]]
	[[Category: Sun, G]]		[[Category: Sun, G]]
-	[[Category: Liu, Y]]
	[[Category: Luo, M]]		[[Category: Luo, M]]
		+	[[Category: Li, Z]]
		+	[[Category: Liu, Y]]
	[[Category: Sun, Y]]		[[Category: Sun, Y]]
	[[Category: Deng, Z]]		[[Category: Deng, Z]]
	[[Category: Hu, C]]		[[Category: Hu, C]]

OCA: Protected "6m4p" [edit=sysop:move=sysop]

2020-03-18T08:18:14Z

Protected "6m4p" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:18, 18 March 2020

OCA: New page: '''Unreleased structure''' The entry 6m4p is ON HOLD Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y. Description: Uncovering the Bio...

2020-03-18T08:18:13Z

New page: '''Unreleased structure''' The entry 6m4p is ON HOLD Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y. Description: Uncovering the Bio...

New page

'''Unreleased structure'''

The entry 6m4p is ON HOLD

Authors: Sun, G., Hu, C., Mei, Q., Luo, M., Chen, X., Li, Z., Liu, Y., Deng, Z., Zhang, Z., Sun, Y.

Description: Uncovering the Biosynthetic Pathway of the Methylenedioxy Bridge in Streptovaricins: from Damavaricin C to Streptovaricin C by Cytochrome P450 Monooxygenases
[[Category: Unreleased Structures]]
[[Category: Li, Z]]
[[Category: Zhang, Z]]
[[Category: Chen, X]]
[[Category: Mei, Q]]
[[Category: Sun, G]]
[[Category: Liu, Y]]
[[Category: Luo, M]]
[[Category: Sun, Y]]
[[Category: Deng, Z]]
[[Category: Hu, C]]