7f5q - Revision history

OCA at 07:49, 1 May 2024

OCA — Wed, 01 May 2024 07:49:12 GMT

←Older revision		Revision as of 07:49, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A509GV09_9ROSI A0A509GV09_9ROSI]		[https://www.uniprot.org/uniprot/A0A509GV09_9ROSI A0A509GV09_9ROSI]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Peptide ligases are versatile enzymes that can be utilized for precise protein conjugation for bioengineering applications. Hyperactive peptide asparaginyl ligases (PALs), such as butelase-1, belong to a small class of enzymes from cyclotide-producing plants that can perform site-specific, rapid ligation reactions after a target peptide Asx (asparagine/aspartic acid) residue binds to the active site of the ligase. How PALs specifically recognize their polypeptide substrates has remained elusive, especially at the prime binding side of the enzyme. Here we report crystal structures that capture VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzyme's S1 pocket and why a hydrophobic residue is required at the P2' position. Beside illustrating the anchoring role played by P1 and P2' residues, these results uncover a role for the Gatekeeper residue at the surface of the S2 pocket in shifting the non-prime portion of the substrate and, as a result, the activity towards ligation or hydrolysis. These results suggest a picture for proenzyme maturation in the vacuole and will inform the rational design of peptide ligases with tailored specificities.
-
-	Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase.,Hu S, El Sahili A, Kishore S, Wong YH, Hemu X, Goh BC, Sang Z, Wang Z, Tam JP, Liu CF, Lescar J Plant Cell. 2022 Sep 13:koac281. doi: 10.1093/plcell/koac281. PMID:36099055<ref>PMID:36099055</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7f5q" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:56, 15 November 2023

OCA — Wed, 15 Nov 2023 10:56:44 GMT

←Older revision		Revision as of 10:56, 15 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7f5q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viola_philippica Viola philippica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F5Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[7f5q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viola_philippica Viola philippica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F5Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HD0:(2S)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-(1H-imidazol-5-yl)propanoic+acid'>HD0</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HD0:(2S)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-(1H-imidazol-5-yl)propanoic+acid'>HD0</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f5q OCA], [https://pdbe.org/7f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f5q RCSB], [https://www.ebi.ac.uk/pdbsum/7f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f5q 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=7f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f5q OCA], [https://pdbe.org/7f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f5q RCSB], [https://www.ebi.ac.uk/pdbsum/7f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f5q ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:52, 30 November 2022

OCA — Wed, 30 Nov 2022 10:52:53 GMT

←Older revision		Revision as of 10:52, 30 November 2022
Line 1:		Line 1:

-	==~~n/a~~==	+	==An active enzyme from the plant Viola yedoensis==
-	<StructureSection load='7f5q' size='340' side='right'caption='[[7f5q]]' scene=''>	+	<StructureSection load='7f5q' size='340' side='right'caption='[[7f5q]], [[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=7F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7f5q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Viola_philippica Viola philippica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F5Q FirstGlance]. <br>
-	</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=7f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f5q OCA], [https://pdbe.org/7f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f5q RCSB], [https://www.ebi.ac.uk/pdbsum/7f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f5q 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HD0:(2S)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-(1H-imidazol-5-yl)propanoic+acid'>HD0</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f5q OCA], [https://pdbe.org/7f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f5q RCSB], [https://www.ebi.ac.uk/pdbsum/7f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f5q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A509GV09_9ROSI A0A509GV09_9ROSI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptide ligases are versatile enzymes that can be utilized for precise protein conjugation for bioengineering applications. Hyperactive peptide asparaginyl ligases (PALs), such as butelase-1, belong to a small class of enzymes from cyclotide-producing plants that can perform site-specific, rapid ligation reactions after a target peptide Asx (asparagine/aspartic acid) residue binds to the active site of the ligase. How PALs specifically recognize their polypeptide substrates has remained elusive, especially at the prime binding side of the enzyme. Here we report crystal structures that capture VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzyme's S1 pocket and why a hydrophobic residue is required at the P2' position. Beside illustrating the anchoring role played by P1 and P2' residues, these results uncover a role for the Gatekeeper residue at the surface of the S2 pocket in shifting the non-prime portion of the substrate and, as a result, the activity towards ligation or hydrolysis. These results suggest a picture for proenzyme maturation in the vacuole and will inform the rational design of peptide ligases with tailored specificities.
		+
		+	Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase.,Hu S, El Sahili A, Kishore S, Wong YH, Hemu X, Goh BC, Sang Z, Wang Z, Tam JP, Liu CF, Lescar J Plant Cell. 2022 Sep 13:koac281. doi: 10.1093/plcell/koac281. PMID:36099055<ref>PMID:36099055</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7f5q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~N/a~~]]	+	[[Category: Viola philippica]]
		+	[[Category: Hu S]]
		+	[[Category: Lescar J]]
		+	[[Category: Sahili A]]

OCA at 07:25, 29 June 2022

OCA — Wed, 29 Jun 2022 07:25:38 GMT

←Older revision		Revision as of 07:25, 29 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7f5q ~~is ON HOLD until Paper Publication~~	+	==n/a==
-		+	<StructureSection load='7f5q' size='340' side='right'caption='[[7f5q]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F5Q FirstGlance]. <br>
-	~~Description~~:	+	</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=7f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f5q OCA], [https://pdbe.org/7f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f5q RCSB], [https://www.ebi.ac.uk/pdbsum/7f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f5q ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: N/a]]

OCA at 05:05, 25 August 2021

OCA — Wed, 25 Aug 2021 05:05:29 GMT

←Older revision		Revision as of 05:05, 25 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7f5q is ON HOLD	+	The entry 7f5q is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7f5q" [edit=sysop:move=sysop]

OCA — Fri, 02 Jul 2021 02:24:49 GMT

Protected "7f5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:24, 2 July 2021

OCA: New page: '''Unreleased structure''' The entry 7f5q is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 02 Jul 2021 02:24:48 GMT

New page: '''Unreleased structure''' The entry 7f5q is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7f5q is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]