OCA at 13:39, 24 January 2024

OCA — Wed, 24 Jan 2024 13:39:27 GMT

←Older revision		Revision as of 13:39, 24 January 2024
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-	====	+	==Het-Ncap - De novo designed three-helix heterodimer with Cysteine at the Ncap position of the alpha-helix==
-	<StructureSection load='6z0m' size='340' side='right'caption='[[6z0m]]' scene=''>	+	<StructureSection load='6z0m' size='340' side='right'caption='[[6z0m]], [[Resolution\|resolution]] 1.45Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z0m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z0M 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=6z0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z0m OCA], [https://pdbe.org/6z0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z0m RCSB], [https://www.ebi.ac.uk/pdbsum/6z0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z0m ProSAT]</span></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]] 1.45Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6z0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z0m OCA], [https://pdbe.org/6z0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z0m RCSB], [https://www.ebi.ac.uk/pdbsum/6z0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z0m ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the alpha-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the alpha-helix N-terminus in a designed three-alpha-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-(alpha)thioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
		+
		+	Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of alpha-Helix As Oxyanion-Binding Site.,Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V J Am Chem Soc. 2021 Mar 10;143(9):3330-3339. doi: 10.1021/jacs.0c10053. Epub 2021 , Feb 26. PMID:33635059<ref>PMID:33635059</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6z0m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: DeGrado WF]]
		+	[[Category: McEwen AG]]
		+	[[Category: Naudin EA]]
		+	[[Category: Poussin-Courmontagne P]]
		+	[[Category: Torbeev V]]

OCA at 06:43, 17 March 2021

OCA — Wed, 17 Mar 2021 06:43:38 GMT

←Older revision		Revision as of 06:43, 17 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6z0m ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6z0m' size='340' side='right'caption='[[6z0m]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= 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=6z0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z0m OCA], [https://pdbe.org/6z0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z0m RCSB], [https://www.ebi.ac.uk/pdbsum/6z0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z0m ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 07:40, 22 July 2020

OCA — Wed, 22 Jul 2020 07:40:27 GMT

←Older revision		Revision as of 07:40, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6z0m is ON HOLD	+	The entry 6z0m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6z0m" [edit=sysop:move=sysop]

OCA — Wed, 20 May 2020 04:29:52 GMT

Protected "6z0m" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:29, 20 May 2020

OCA: New page: '''Unreleased structure''' The entry 6z0m is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 May 2020 04:29:50 GMT

New page: '''Unreleased structure''' The entry 6z0m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6z0m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6z0m - Revision history

OCA at 13:39, 24 January 2024

OCA at 06:43, 17 March 2021

OCA at 07:40, 22 July 2020

OCA: Protected "6z0m" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6z0m is ON HOLD Authors: Description: Category: Unreleased Structures