5btu - Revision history

OCA at 06:08, 7 June 2023

2023-06-07T06:08:04Z

←Older revision		Revision as of 06:08, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5btu' size='340' side='right'caption='[[5btu]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5btu' size='340' side='right'caption='[[5btu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5btu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~'streptomyces_rugosporus' 'streptomyces~~ rugosporus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BTU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5btu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rugosporus Streptomyces rugosporus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BTU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=~~PEG~~:~~DI(HYDROXYETHYL)ETHER~~'>~~PEG~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=5btu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5btu OCA], [https://pdbe.org/5btu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5btu RCSB], [https://www.ebi.ac.uk/pdbsum/5btu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5btu ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bu3\|5bu3]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrI4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=295838 'Streptomyces rugosporus'])</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=5btu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5btu OCA], [~~http~~://pdbe.org/5btu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5btu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5btu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5btu ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PYRI4_STRRG PYRI4_STRRG] Involved in the biosynthesis of the spirotetramate antibiotics pyrroindomycins. Catalyzes the intramolecular cyclization forming the spiro-conjugate moiety in pyrroindomycins, via an exo-selective [4+2] cycloaddition reaction.<ref>PMID:25730548</ref> <ref>PMID:26877021</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces rugosporus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Guo, Y~~]]	+	[[Category: Streptomyces rugosporus]]
-	[[Category: ~~Liu, J~~]]	+	[[Category: Guo Y]]
-	[[Category: ~~Pan, L~~]]	+	[[Category: Liu J]]
-	[[Category: ~~Beta-barrel]]~~	+	[[Category: Pan L]]
-	~~[[Category: Diels-alderase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Pyrroindomycin~~]]	+

OCA at 11:00, 18 March 2020

2020-03-18T11:00:26Z

←Older revision		Revision as of 11:00, 18 March 2020
Line 1:		Line 1:

	==The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins==		==The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins==
-	<StructureSection load='5btu' size='340' side='right' caption='[[5btu]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5btu' size='340' side='right'caption='[[5btu]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5btu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BTU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5btu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'streptomyces_rugosporus' 'streptomyces rugosporus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BTU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bu3\|5bu3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bu3\|5bu3]]</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=5btu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5btu OCA], [http://pdbe.org/5btu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5btu RCSB], [http://www.ebi.ac.uk/pdbsum/5btu PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrI4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=295838 'Streptomyces rugosporus'])</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=5btu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5btu OCA], [http://pdbe.org/5btu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5btu RCSB], [http://www.ebi.ac.uk/pdbsum/5btu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5btu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces rugosporus]]
		+	[[Category: Large Structures]]
	[[Category: Guo, Y]]		[[Category: Guo, Y]]
	[[Category: Liu, J]]		[[Category: Liu, J]]

OCA at 18:12, 26 February 2016

2016-02-26T18:12:14Z

←Older revision		Revision as of 18:12, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5btu is ~~ON HOLD until Paper~~ Publication	+	==The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins==
		+	<StructureSection load='5btu' size='340' side='right' caption='[[5btu]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5btu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BTU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bu3\|5bu3]]</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=5btu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5btu OCA], [http://pdbe.org/5btu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5btu RCSB], [http://www.ebi.ac.uk/pdbsum/5btu PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Diels-Alder [4 + 2] cycloaddition reaction is one of the most powerful and elegant organic synthesis methods for forming 6-membered molecules and has been known for nearly a century. However, whether and how enzymes catalyze this type of reaction is still not completely clear. Here we focus on PyrI4, an enzyme found in the biosynthetic pathway of pyrroindomycins where it catalyzes the formation of a spiro-conjugate via an enzyme-dependent exo-selective [4 + 2] cycloaddition reaction. We report the crystal structures of PyrI4 alone and in complex with its product. Comparative analysis of these structures, combined with biochemical analysis, lead us to propose a unique trapping mechanism whereby the lid-like action of the N-terminal tail imposes conformational constraints on the beta barrel catalytic core, which enhances the proximity and polarization effects of reactive groups (1,3-diene and alkene) to drive cyclization in a regio- and stereo-specific manner. This work represents an important step toward the wider application of enzyme-catalyzed [4 + 2] cyclization for synthetic purposes.

-	~~Authors: Pan, L~~., ~~Guo~~, Y., Liu, J.	+	Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4.,Zheng Q, Guo Y, Yang L, Zhao Z, Wu Z, Zhang H, Liu J, Cheng X, Wu J, Yang H, Jiang H, Pan L, Liu W Cell Chem Biol. 2016 Feb 8. pii: S2451-9456(16)30006-X. doi:, 10.1016/j.chembiol.2016.01.005. PMID:26877021<ref>PMID:26877021</ref>

-	~~Description: The structure~~ of ~~Diels-Alderase PyrI4 in~~ the ~~biosynthetic pathway~~ of ~~pyrroindomycins~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5btu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Guo, Y]]		[[Category: Guo, Y]]
-	[[Category: Pan, L]]
	[[Category: Liu, J]]		[[Category: Liu, J]]
		+	[[Category: Pan, L]]
		+	[[Category: Beta-barrel]]
		+	[[Category: Diels-alderase]]
		+	[[Category: Lyase]]
		+	[[Category: Pyrroindomycin]]

OCA at 10:12, 16 December 2015

2015-12-16T10:12:00Z

←Older revision		Revision as of 10:12, 16 December 2015
Line 7:		Line 7:
	Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins		Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Guo, Y]]
	[[Category: Pan, L]]		[[Category: Pan, L]]
	[[Category: Liu, J]]		[[Category: Liu, J]]
-	[[Category: Guo, Y]]

OCA at 12:44, 2 December 2015

2015-12-02T12:44:05Z

←Older revision		Revision as of 12:44, 2 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5btu is ON HOLD	+	The entry 5btu is ON HOLD until Paper Publication

	Authors: Pan, L., Guo, Y., Liu, J.		Authors: Pan, L., Guo, Y., Liu, J.

OCA at 13:53, 17 June 2015

2015-06-17T13:53:40Z

←Older revision		Revision as of 13:53, 17 June 2015
Line 3:		Line 3:
	The entry 5btu is ON HOLD		The entry 5btu is ON HOLD

-	Authors: ~~Lifeng~~ Pan, ~~Yujiao~~ Guo, ~~Jianping~~ Liu	+	Authors: Pan, L., Guo, Y., Liu, J.

	Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins		Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Lifeng~~ Pan, ~~Yujiao~~ Guo, ~~Jianping Liu~~]]	+	[[Category: Pan, L]]
		+	[[Category: Liu, J]]
		+	[[Category: Guo, Y]]

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

2015-06-10T13:03:28Z

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

←Older revision

Revision as of 13:03, 10 June 2015

OCA: New page: '''Unreleased structure''' The entry 5btu is ON HOLD Authors: Lifeng Pan, Yujiao Guo, Jianping Liu Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyr...

2015-06-10T13:03:27Z

New page: '''Unreleased structure''' The entry 5btu is ON HOLD Authors: Lifeng Pan, Yujiao Guo, Jianping Liu Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyr...

New page

'''Unreleased structure'''

The entry 5btu is ON HOLD

Authors: Lifeng Pan, Yujiao Guo, Jianping Liu

Description: The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins
[[Category: Unreleased Structures]]
[[Category: Lifeng Pan, Yujiao Guo, Jianping Liu]]