5uzw - Revision history

OCA at 14:30, 6 March 2024

OCA — Wed, 06 Mar 2024 14:30:31 GMT

←Older revision		Revision as of 14:30, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5uzw' size='340' side='right'caption='[[5uzw]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='5uzw' size='340' side='right'caption='[[5uzw]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uzw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uzw]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Gypsophila_vaccaria Gypsophila vaccaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UZW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZPR:N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL'>ZPR</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]] 2.82Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uw3\|5uw3]], [[5uw5\|5uw5]], [[5uw6\|5uw6]], [[5uw7\|5uw7]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZPR:N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL'>ZPR</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=5uzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzw OCA], [~~http~~://pdbe.org/5uzw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uzw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uzw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzw 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=5uzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzw OCA], [https://pdbe.org/5uzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uzw RCSB], [https://www.ebi.ac.uk/pdbsum/5uzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzw ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/R4P353_GYPVA R4P353_GYPVA]
-	Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.	+
-		+
-	~~Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.,Chekan JR, Estrada P, Covello PS, Nair SK Proc Natl Acad Sci U S A. 2017 Jun 20;114(25)~~:~~6551-6556. doi:, 10.1073~~/~~pnas.1620499114. Epub 2017 Jun 5. PMID:28584123<ref>PMID:28584123<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5uzw" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gypsophila vaccaria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chekan~~, J R~~]]	+	[[Category: Chekan JR]]
-	[[Category: Nair~~, S K]]~~	+	[[Category: Nair SK]]
-	~~[[Category: Cyclase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Natural product]]~~	+
-	~~[[Category: Orbitide~~]]	+

OCA at 08:28, 30 September 2020

OCA — Wed, 30 Sep 2020 08:28:18 GMT

←Older revision		Revision as of 08:28, 30 September 2020
Line 1:		Line 1:

	==PCY1 G696Insertion Variant in Complex with Follower Peptide and the Covalent Inhibitor ZPP==		==PCY1 G696Insertion Variant in Complex with Follower Peptide and the Covalent Inhibitor ZPP==
-	<StructureSection load='5uzw' size='340' side='right' caption='[[5uzw]], [[Resolution\|resolution]] 2.82Å' scene=''>	+	<StructureSection load='5uzw' size='340' side='right'caption='[[5uzw]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uzw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uzw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UZW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZPR:N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL'>ZPR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZPR:N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL'>ZPR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uw3\|5uw3]], [[5uw5\|5uw5]], [[5uw6\|5uw6]], [[5uw7\|5uw7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uw3\|5uw3]], [[5uw5\|5uw5]], [[5uw6\|5uw6]], [[5uw7\|5uw7]]</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=5uzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzw OCA], [http://pdbe.org/5uzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uzw RCSB], [http://www.ebi.ac.uk/pdbsum/5uzw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzw 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=5uzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzw OCA], [http://pdbe.org/5uzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uzw RCSB], [http://www.ebi.ac.uk/pdbsum/5uzw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chekan, J R]]		[[Category: Chekan, J R]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]

OCA at 08:15, 3 August 2017

OCA — Thu, 03 Aug 2017 08:15:42 GMT

←Older revision		Revision as of 08:15, 3 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uzw is ~~ON HOLD until Paper~~ Publication	+	==PCY1 G696Insertion Variant in Complex with Follower Peptide and the Covalent Inhibitor ZPP==
		+	<StructureSection load='5uzw' size='340' side='right' caption='[[5uzw]], [[Resolution\|resolution]] 2.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uzw]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UZW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZPR:N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL'>ZPR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uw3\|5uw3]], [[5uw5\|5uw5]], [[5uw6\|5uw6]], [[5uw7\|5uw7]]</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=5uzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzw OCA], [http://pdbe.org/5uzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uzw RCSB], [http://www.ebi.ac.uk/pdbsum/5uzw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzw ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.

-	~~Authors:~~ Chekan, ~~J.R.~~, ~~Nair~~, S.K.	+	Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.,Chekan JR, Estrada P, Covello PS, Nair SK Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6551-6556. doi:, 10.1073/pnas.1620499114. Epub 2017 Jun 5. PMID:28584123<ref>PMID:28584123</ref>

-	~~Description: PCY1 G696Insertion Variant in Complex with Follower Peptide and~~ the ~~Covalent Inhibitor ZPP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Nair, S.K]]	+	<div class="pdbe-citations 5uzw" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Chekan, J.R~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chekan, J R]]
		+	[[Category: Nair, S K]]
		+	[[Category: Cyclase]]
		+	[[Category: Lyase]]
		+	[[Category: Natural product]]
		+	[[Category: Orbitide]]

OCA at 19:33, 15 March 2017

OCA — Wed, 15 Mar 2017 19:33:55 GMT

←Older revision		Revision as of 19:33, 15 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Chekan, J.R., Nair, S.K.		Authors: Chekan, J.R., Nair, S.K.

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

OCA — Thu, 09 Mar 2017 15:09:43 GMT

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

←Older revision

Revision as of 15:09, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5uzw is ON HOLD Authors: Chekan, J.R., Nair, S.K. Description: PCY1 G696Insertion Variant in Complex with Follower Peptide and the Covalent Inhibit...

OCA — Thu, 09 Mar 2017 15:09:42 GMT

New page: '''Unreleased structure''' The entry 5uzw is ON HOLD Authors: Chekan, J.R., Nair, S.K. Description: PCY1 G696Insertion Variant in Complex with Follower Peptide and the Covalent Inhibit...

New page

'''Unreleased structure'''

The entry 5uzw is ON HOLD

Authors: Chekan, J.R., Nair, S.K.

Description: PCY1 G696Insertion Variant in Complex with Follower Peptide and the Covalent Inhibitor ZPP
[[Category: Unreleased Structures]]
[[Category: Nair, S.K]]
[[Category: Chekan, J.R]]