3u13: Difference between revisions

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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3u13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u13 OCA], [https://pdbe.org/3u13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u13 RCSB], [https://www.ebi.ac.uk/pdbsum/3u13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u13 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=3u13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u13 OCA], [https://pdbe.org/3u13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u13 RCSB], [https://www.ebi.ac.uk/pdbsum/3u13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u13 ProSAT]</span></td></tr>
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== Publication Abstract from PubMed ==
Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.
Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.,Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJ, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D J Am Chem Soc. 2012 Oct 3;134(39):16197-206. doi: 10.1021/ja3037367. Epub 2012, Sep 21. PMID:22871159<ref>PMID:22871159</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3u13" style="background-color:#fffaf0;"></div>
== References ==
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Revision as of 16:45, 14 March 2024

Crystal Structure of de Novo design of cystein esterase ECH13 at the resolution 1.6A, Northeast Structural Genomics Consortium Target OR51Crystal Structure of de Novo design of cystein esterase ECH13 at the resolution 1.6A, Northeast Structural Genomics Consortium Target OR51

Structural highlights

3u13 is a 1 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

3u13, resolution 1.60Å

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