6z0m: Difference between revisions
New page: '''Unreleased structure''' The entry 6z0m is ON HOLD Authors: Description: Category: Unreleased Structures |
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The | ==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]], [[Resolution|resolution]] 1.45Å' scene=''> | |||
== Structural highlights == | |||
<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='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> | |||
<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> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6z0m" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: DeGrado WF]] | |||
[[Category: McEwen AG]] | |||
[[Category: Naudin EA]] | |||
[[Category: Poussin-Courmontagne P]] | |||
[[Category: Torbeev V]] | |||
Latest revision as of 16:39, 24 January 2024
Het-Ncap - De novo designed three-helix heterodimer with Cysteine at the Ncap position of the alpha-helixHet-Ncap - De novo designed three-helix heterodimer with Cysteine at the Ncap position of the alpha-helix
Structural highlights
Publication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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