3nyd: Difference between revisions
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==Crystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro Benzotriazole== | ==Crystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro Benzotriazole== | ||
<StructureSection load='3nyd' size='340' side='right' caption='[[3nyd]], [[Resolution|resolution]] 1.23Å' scene=''> | <StructureSection load='3nyd' size='340' side='right'caption='[[3nyd]], [[Resolution|resolution]] 1.23Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3nyd]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3nyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Theau Theau]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYD FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Xylanase I, XYNA ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Xylanase I, XYNA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5087 THEAU])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></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=3nyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyd OCA], [https://pdbe.org/3nyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyd RCSB], [https://www.ebi.ac.uk/pdbsum/3nyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Endo-1,4-beta-xylanase]] | [[Category: Endo-1,4-beta-xylanase]] | ||
[[Category: Large Structures]] | |||
[[Category: Theau]] | [[Category: Theau]] | ||
[[Category: Kaiser, J T]] | [[Category: Kaiser, J T]] | ||
Revision as of 10:11, 12 May 2022
Crystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro BenzotriazoleCrystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro Benzotriazole
Structural highlights
Publication Abstract from PubMedA general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes. Iterative approach to computational enzyme design.,Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN, Mayo SL Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3790-5. Epub 2012 Feb 22. PMID:22357762[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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