5bu3 - Revision history

OCA at 16:05, 8 November 2023

OCA — Wed, 08 Nov 2023 16:05:20 GMT

←Older revision		Revision as of 16:05, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bu3]] is a 4 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=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bu3]] is a 4 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=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.897Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [https://pdbe.org/5bu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [https://www.ebi.ac.uk/pdbsum/5bu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bu3 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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [https://pdbe.org/5bu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [https://www.ebi.ac.uk/pdbsum/5bu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bu3 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:08, 7 June 2023

OCA — Wed, 07 Jun 2023 06:08:20 GMT

←Older revision		Revision as of 06:08, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5bu3' size='340' side='right'caption='[[5bu3]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5bu3' size='340' side='right'caption='[[5bu3]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bu3]] is a 4 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=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bu3]] is a 4 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=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5btu\|5btu]]</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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [https://pdbe.org/5bu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [https://www.ebi.ac.uk/pdbsum/5bu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bu3 ProSAT]</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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [~~http~~://pdbe.org/5bu3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bu3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bu3 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 22:		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: ~~Complex]]~~	+	[[Category: Pan L]]
-	~~[[Category: Diels-alderase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 11:00, 18 March 2020

OCA — Wed, 18 Mar 2020 11:00:26 GMT

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

	==Crystal Structure of Diels-Alderase PyrI4 in complex with its product==		==Crystal Structure of Diels-Alderase PyrI4 in complex with its product==
-	<StructureSection load='5bu3' size='340' side='right' caption='[[5bu3]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5bu3' size='340' side='right'caption='[[5bu3]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bu3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bu3]] is a 4 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=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5btu\|5btu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5btu\|5btu]]</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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [http://pdbe.org/5bu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [http://www.ebi.ac.uk/pdbsum/5bu3 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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [http://pdbe.org/5bu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [http://www.ebi.ac.uk/pdbsum/5bu3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bu3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces rugosporus]]
		+	[[Category: Large Structures]]
	[[Category: Guo, Y]]		[[Category: Guo, Y]]
	[[Category: Liu, J]]		[[Category: Liu, J]]

OCA at 18:09, 26 February 2016

OCA — Fri, 26 Feb 2016 18:09:55 GMT

←Older revision		Revision as of 18:09, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5bu3 is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Diels-Alderase PyrI4 in complex with its product==
		+	<StructureSection load='5bu3' size='340' side='right' caption='[[5bu3]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5bu3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BU3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4W9:(4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione'>4W9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5btu\|5btu]]</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=5bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bu3 OCA], [http://pdbe.org/5bu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bu3 RCSB], [http://www.ebi.ac.uk/pdbsum/5bu3 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:~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5bu3" 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: Complex]]
		+	[[Category: Diels-alderase]]
		+	[[Category: Lyase]]

OCA at 10:12, 16 December 2015

OCA — Wed, 16 Dec 2015 10:12:06 GMT

←Older revision		Revision as of 10:12, 16 December 2015
Line 7:		Line 7:
	Description:		Description:
	[[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

OCA — Wed, 02 Dec 2015 12:44:11 GMT

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

-	The entry 5bu3 is ON HOLD	+	The entry 5bu3 is ON HOLD until Paper Publication

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

OCA at 13:54, 17 June 2015

OCA — Wed, 17 Jun 2015 13:54:05 GMT

←Older revision		Revision as of 13:54, 17 June 2015
Line 3:		Line 3:
	The entry 5bu3 is ON HOLD		The entry 5bu3 is ON HOLD

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

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Lifeng~~ Pan, ~~Yujiao~~ Guo, ~~Jianping Liu~~]]	+	[[Category: Pan, L]]
		+	[[Category: Liu, J]]
		+	[[Category: Guo, Y]]

OCA: Protected "5bu3" [edit=sysop:move=sysop]

OCA — Wed, 10 Jun 2015 13:03:57 GMT

Protected "5bu3" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:03, 10 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bu3 is ON HOLD Authors: Lifeng Pan, Yujiao Guo, Jianping Liu Description: Category: Unreleased Structures [[Category: Lifeng Pan, Yujiao Guo,...

OCA — Wed, 10 Jun 2015 13:03:56 GMT

New page: '''Unreleased structure''' The entry 5bu3 is ON HOLD Authors: Lifeng Pan, Yujiao Guo, Jianping Liu Description: Category: Unreleased Structures [[Category: Lifeng Pan, Yujiao Guo,...

New page

'''Unreleased structure'''

The entry 5bu3 is ON HOLD

Authors: Lifeng Pan, Yujiao Guo, Jianping Liu

Description:
[[Category: Unreleased Structures]]
[[Category: Lifeng Pan, Yujiao Guo, Jianping Liu]]