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| | ==Crystal Structure of an Inactive Kemp Elimination Design HG-1== | | ==Crystal Structure of an Inactive Kemp Elimination Design HG-1== |
| - | <StructureSection load='3o2l' size='340' side='right' caption='[[3o2l]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3o2l' size='340' side='right'caption='[[3o2l]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3o2l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O2L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O2L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3o2l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O2L FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nyd|3nyd]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XYNA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5087 Thermoascus aurantiacus])</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=3o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o2l OCA], [https://pdbe.org/3o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o2l RCSB], [https://www.ebi.ac.uk/pdbsum/3o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o2l ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr> | + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o2l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o2l RCSB], [http://www.ebi.ac.uk/pdbsum/3o2l PDBsum]</span></td></tr>
| + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/XYNA_THEAU XYNA_THEAU] |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed == | + | |
| - | A 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.
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| - | 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<ref>PMID:22357762</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Endo-1,4-beta-xylanase]] | + | [[Category: Large Structures]] |
| | [[Category: Thermoascus aurantiacus]] | | [[Category: Thermoascus aurantiacus]] |
| - | [[Category: Mayo, S L.]] | + | [[Category: Mayo SL]] |
| - | [[Category: Privett, H K.]] | + | [[Category: Privett HK]] |
| - | [[Category: Thomas, L M.]] | + | [[Category: Thomas LM]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Kemp eliminase]]
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| - | [[Category: Kemp elimination]]
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| - | [[Category: Tim barrel]]
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