3uxd: Difference between revisions
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==Designed protein KE59 R1 7/10H with dichlorobenzotriazole (DBT)== | ==Designed protein KE59 R1 7/10H with dichlorobenzotriazole (DBT)== | ||
<StructureSection load='3uxd' size='340' side='right' caption='[[3uxd]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='3uxd' size='340' side='right'caption='[[3uxd]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3uxd]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3uxd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UXD FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0CU:5,7-DICHLORO-1H-BENZOTRIAZOLE'>0CU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0CU:5,7-DICHLORO-1H-BENZOTRIAZOLE'>0CU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3uxa|3uxa]], [[3uy7|3uy7]], [[3uy8|3uy8]], [[3uyc|3uyc]], [[3uz5|3uz5]], [[3uzj|3uzj]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3uxa|3uxa]], [[3uy7|3uy7]], [[3uy8|3uy8]], [[3uyc|3uyc]], [[3uz5|3uz5]], [[3uzj|3uzj]]</div></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxd OCA], [https://pdbe.org/3uxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uxd RCSB], [https://www.ebi.ac.uk/pdbsum/3uxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uxd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Bacillus coli migula 1895]] | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Large Structures]] | |||
[[Category: Albeck, S]] | [[Category: Albeck, S]] | ||
[[Category: Baker, D]] | [[Category: Baker, D]] | ||
Revision as of 11:14, 20 July 2022
Designed protein KE59 R1 7/10H with dichlorobenzotriazole (DBT)Designed protein KE59 R1 7/10H with dichlorobenzotriazole (DBT)
Structural highlights
Publication Abstract from PubMedComputational design is a test of our understanding of enzyme catalysis and a means of engineering novel, tailor-made enzymes. While the de novo computational design of catalytically efficient enzymes remains a challenge, designed enzymes may comprise unique starting points for further optimization by directed evolution. Directed evolution of two computationally designed Kemp eliminases, KE07 and KE70, led to low to moderately efficient enzymes (k(cat)/K(m) values of </= 5 10(4) M(-1)s(-1)). Here we describe the optimization of a third design, KE59. Although KE59 was the most catalytically efficient Kemp eliminase from this design series (by k(cat)/K(m), and by catalyzing the elimination of nonactivated benzisoxazoles), its impaired stability prevented its evolutionary optimization. To boost KE59's evolvability, stabilizing consensus mutations were included in the libraries throughout the directed evolution process. The libraries were also screened with less activated substrates. Sixteen rounds of mutation and selection led to > 2,000-fold increase in catalytic efficiency, mainly via higher k(cat) values. The best KE59 variants exhibited k(cat)/K(m) values up to 0.6 10(6) M(-1)s(-1), and k(cat)/k(uncat) values of </= 10(7) almost regardless of substrate reactivity. Biochemical, structural, and molecular dynamics (MD) simulation studies provided insights regarding the optimization of KE59. Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies. Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.,Khersonsky O, Kiss G, Rothlisberger D, Dym O, Albeck S, Houk KN, Baker D, Tawfik DS Proc Natl Acad Sci U S A. 2012 Jun 8. PMID:22685214[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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