6dnj: Difference between revisions
New page: '''Unreleased structure''' The entry 6dnj is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 28 round... |
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==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5== | |||
<StructureSection load='6dnj' size='340' side='right'caption='[[6dnj]], [[Resolution|resolution]] 1.65Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6dnj]] is a 1 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=6DNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DNJ 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]] 1.65Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H5J:5-nitro-1,2-benzoxazole'>H5J</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6dnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dnj OCA], [https://pdbe.org/6dnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dnj RCSB], [https://www.ebi.ac.uk/pdbsum/6dnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dnj ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis. | |||
The evolution of multiple active site configurations in a designed enzyme.,Hong NS, Petrovic D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ Nat Commun. 2018 Sep 25;9(1):3900. doi: 10.1038/s41467-018-06305-y. PMID:30254369<ref>PMID:30254369</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6dnj" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
*[[Kemp eliminase|Kemp eliminase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Carr PD]] | |||
[[Category: Hong N-S]] | |||
[[Category: Jackson CJ]] | |||
Latest revision as of 09:10, 11 October 2023
Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5
Structural highlights
Publication Abstract from PubMedDevelopments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis. The evolution of multiple active site configurations in a designed enzyme.,Hong NS, Petrovic D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ Nat Commun. 2018 Sep 25;9(1):3900. doi: 10.1038/s41467-018-06305-y. PMID:30254369[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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