3nyd: Difference between revisions

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-[[Image:3nyd.jpg|left|200px]]
-<!--
+==Crystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro Benzotriazole==
-The line below this paragraph, containing "STRUCTURE_3nyd", creates the "Structure Box" on the page.
+<StructureSection load='3nyd' size='340' side='right'caption='[[3nyd]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3nyd]] is a 2 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=3NYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.23&#8491;</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>
-{{STRUCTURE_3nyd|  PDB=3nyd  |  SCENE=  }}
+<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>
+== Function ==
+[https://www.uniprot.org/uniprot/XYNA_THEAU XYNA_THEAU]
+<div style="background-color:#fffaf0;">
+== 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.
-===Crystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro Benzotriazole===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[3nyd]] is a 2 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=3NYD OCA].
+<div class="pdbe-citations 3nyd" style="background-color:#fffaf0;"></div>
-[[Category: Endo-1,4-beta-xylanase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermoascus aurantiacus]]
-[[Category: Kaiser, J T.]]
+[[Category: Kaiser JT]]
-[[Category: Lee, T M.]]
+[[Category: Lee TM]]
-[[Category: Mayo, S L.]]
+[[Category: Mayo SL]]
-[[Category: Privett, H K.]]
+[[Category: Privett HK]]
-[[Category: Hydrolase]]
-[[Category: Kemp elimination enzyme]]
-[[Category: Tim barrel]]