5o3u - Revision history

OCA at 07:27, 1 May 2024

OCA — Wed, 01 May 2024 07:27:41 GMT

←Older revision		Revision as of 07:27, 1 May 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/R4P353_GYPVA R4P353_GYPVA]		[https://www.uniprot.org/uniprot/R4P353_GYPVA R4P353_GYPVA]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cyclic ribosomally derived peptides possess diverse bioactivities and are currently of major interest in drug development. However, it can be chemically challenging to synthesize these molecules, hindering the diversification and testing of cyclic peptide leads. Enzymes used in vitro offer a solution to this, however peptide macrocyclization remains the bottleneck. PCY1, involved in the biosynthesis of plant orbitides, belongs to the class of prolyl oligopeptidases and natively displays substrate promiscuity. PCY1 is a promising candidate for in vitro utilization but its substrates require an 11 to 16 residue C-terminal recognition tail. We have characterized PCY1 both kinetically and structurally with multiple substrate complexes revealing for the molecular basis of recognition and catalysis. Using these insights, we have identified a three residue C-terminal extension that replaces the natural recognition tail permitting PCY1 to operate on synthetic substrates. We demonstrate that PCY1 can macrocyclize a variety of substrates with this short tail, including unnatural amino acids and non-amino acids, highlighting PCY1's potential in biocatalysis.
-
-	Characterization of the fast and promiscuous macrocyclase from plant PCY1 enables the use of simple substrates.,Ludewig H, Czekster CM, Oueis E, Munday ES, Arshad M, Synowsky SA, Bent AF, Naismith JH ACS Chem Biol. 2018 Jan 29. doi: 10.1021/acschembio.8b00050. PMID:29377663<ref>PMID:29377663</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5o3u" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:07, 29 November 2023

OCA — Wed, 29 Nov 2023 19:07:17 GMT

←Older revision		Revision as of 19:07, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='5o3u' size='340' side='right'caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='5o3u' size='340' side='right'caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o3u]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gypsophila_vaccaria Gypsophila vaccaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o3u]] 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=5O3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O3U FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Pcy1 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=39387 Gypsophila vaccaria])~~</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]] 1.86Å</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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [~~http~~://pdbe.org/5o3u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u 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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [https://pdbe.org/5o3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [https://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/R4P353_GYPVA R4P353_GYPVA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	[[Category: Gypsophila vaccaria]]		[[Category: Gypsophila vaccaria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bent~~, A F~~]]	+	[[Category: Bent AF]]
-	[[Category: Czekster~~, C M~~]]	+	[[Category: Czekster CM]]
-	[[Category: Ludewig, H]]	+	[[Category: Ludewig H]]
-	[[Category: Naismith~~, J H]]~~	+	[[Category: Naismith JH]]
-	~~[[Category: Beta-propeller]]~~	+
-	~~[[Category: Closed form]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Macrocyclase]]~~	+
-	~~[[Category: Peptidase]]~~	+
-	~~[[Category: Prolyl oligopeptidase]]~~	+
-	~~[[Category: Segetalin biosynthesis~~]]	+

OCA at 06:51, 16 October 2019

OCA — Wed, 16 Oct 2019 06:51:33 GMT

←Older revision		Revision as of 06:51, 16 October 2019
Line 1:		Line 1:

	==Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1==		==Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1==
-	<StructureSection load='5o3u' size='340' side='right' caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>	+	<StructureSection load='5o3u' size='340' side='right'caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o3u]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saponaria_vaccaria Saponaria~~ vaccaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o3u]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Gypsophila_vaccaria Gypsophila vaccaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3U FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pcy1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39387 ~~Saponaria~~ vaccaria])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pcy1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39387 Gypsophila vaccaria])</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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [http://pdbe.org/5o3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [http://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u ProSAT]</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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [http://pdbe.org/5o3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [http://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saponaria~~ vaccaria]]	+	[[Category: Gypsophila vaccaria]]
		+	[[Category: Large Structures]]
	[[Category: Bent, A F]]		[[Category: Bent, A F]]
	[[Category: Czekster, C M]]		[[Category: Czekster, C M]]

OCA at 07:01, 28 March 2018

OCA — Wed, 28 Mar 2018 07:01:39 GMT

←Older revision		Revision as of 07:01, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5o3u' size='340' side='right' caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='5o3u' size='340' side='right' caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o3u]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o3u]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Saponaria_vaccaria Saponaria vaccaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3U FirstGlance]. <br>
-	</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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [http://pdbe.org/5o3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [http://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pcy1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39387 Saponaria vaccaria])</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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [http://pdbe.org/5o3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [http://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Saponaria vaccaria]]
	[[Category: Bent, A F]]		[[Category: Bent, A F]]
	[[Category: Czekster, C M]]		[[Category: Czekster, C M]]

OCA at 06:11, 7 February 2018

OCA — Wed, 07 Feb 2018 06:11:07 GMT

←Older revision		Revision as of 06:11, 7 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o3u is ~~ON HOLD~~	+	==Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1==
		+	<StructureSection load='5o3u' size='340' side='right' caption='[[5o3u]], [[Resolution\|resolution]] 1.86Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o3u]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3U FirstGlance]. <br>
		+	</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=5o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3u OCA], [http://pdbe.org/5o3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3u RCSB], [http://www.ebi.ac.uk/pdbsum/5o3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3u ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cyclic ribosomally derived peptides possess diverse bioactivities and are currently of major interest in drug development. However, it can be chemically challenging to synthesize these molecules, hindering the diversification and testing of cyclic peptide leads. Enzymes used in vitro offer a solution to this, however peptide macrocyclization remains the bottleneck. PCY1, involved in the biosynthesis of plant orbitides, belongs to the class of prolyl oligopeptidases and natively displays substrate promiscuity. PCY1 is a promising candidate for in vitro utilization but its substrates require an 11 to 16 residue C-terminal recognition tail. We have characterized PCY1 both kinetically and structurally with multiple substrate complexes revealing for the molecular basis of recognition and catalysis. Using these insights, we have identified a three residue C-terminal extension that replaces the natural recognition tail permitting PCY1 to operate on synthetic substrates. We demonstrate that PCY1 can macrocyclize a variety of substrates with this short tail, including unnatural amino acids and non-amino acids, highlighting PCY1's potential in biocatalysis.

-	~~Authors: Ludewig~~, H., Czekster, C.M., Bent, A.F.~~, Naismith, J~~.H.	+	Characterization of the fast and promiscuous macrocyclase from plant PCY1 enables the use of simple substrates.,Ludewig H, Czekster CM, Oueis E, Munday ES, Arshad M, Synowsky SA, Bent AF, Naismith JH ACS Chem Biol. 2018 Jan 29. doi: 10.1021/acschembio.8b00050. PMID:29377663<ref>PMID:29377663</ref>

-	~~Description: Structural characterization~~ of the ~~fast and promiscuous macrocyclase from plant~~ -~~PCY1~~-~~S562A bound to Presegetalin F1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Naismith~~, ~~J.H~~]]	+	<div class="pdbe-citations 5o3u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bent, A F]]
		+	[[Category: Czekster, C M]]
	[[Category: Ludewig, H]]		[[Category: Ludewig, H]]
-	[[Category: ~~Bent~~, ~~A.F~~]]	+	[[Category: Naismith, J H]]
-	[[Category: ~~Czekster, C.M~~]]	+	[[Category: Beta-propeller]]
		+	[[Category: Closed form]]
		+	[[Category: Hydrolase]]
		+	[[Category: Macrocyclase]]
		+	[[Category: Peptidase]]
		+	[[Category: Prolyl oligopeptidase]]
		+	[[Category: Segetalin biosynthesis]]

OCA: Protected "5o3u" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:00:47 GMT

Protected "5o3u" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:00, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o3u is ON HOLD Authors: Ludewig, H., Czekster, C.M., Bent, A.F., Naismith, J.H. Description: Structural characterization of the fast and promiscuo...

OCA — Wed, 27 Sep 2017 12:00:46 GMT

New page: '''Unreleased structure''' The entry 5o3u is ON HOLD Authors: Ludewig, H., Czekster, C.M., Bent, A.F., Naismith, J.H. Description: Structural characterization of the fast and promiscuo...

New page

'''Unreleased structure'''

The entry 5o3u is ON HOLD

Authors: Ludewig, H., Czekster, C.M., Bent, A.F., Naismith, J.H.

Description: Structural characterization of the fast and promiscuous macrocyclase from plant -PCY1-S562A bound to Presegetalin F1
[[Category: Unreleased Structures]]
[[Category: Naismith, J.H]]
[[Category: Ludewig, H]]
[[Category: Bent, A.F]]
[[Category: Czekster, C.M]]