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3nyz

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Current revision (10:02, 14 February 2024) (edit) (undo)
 
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<StructureSection load='3nyz' size='340' side='right'caption='[[3nyz]], [[Resolution|resolution]] 1.51&Aring;' scene=''>
<StructureSection load='3nyz' size='340' side='right'caption='[[3nyz]], [[Resolution|resolution]] 1.51&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3nyz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3nyz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYZ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.514&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nz1|3nz1]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyz OCA], [https://pdbe.org/3nyz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyz RCSB], [https://www.ebi.ac.uk/pdbsum/3nyz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyz ProSAT]</span></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=3nyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyz OCA], [https://pdbe.org/3nyz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyz RCSB], [https://www.ebi.ac.uk/pdbsum/3nyz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyz ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/TRPC_SACS2 TRPC_SACS2]
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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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3nyz" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Indole-3-glycerol phosphate synthase|Indole-3-glycerol phosphate synthase]]
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*[[IGPS 3D structures|IGPS 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 35091]]
 
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[[Category: Indole-3-glycerol-phosphate synthase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Kaiser, J T]]
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[[Category: Saccharolobus solfataricus]]
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[[Category: Lee, T M]]
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[[Category: Kaiser JT]]
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[[Category: Mayo, S L]]
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[[Category: Lee TM]]
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[[Category: Privett, H K]]
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[[Category: Mayo SL]]
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[[Category: Kemp elimination enzyme]]
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[[Category: Privett HK]]
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[[Category: Lyase]]
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[[Category: Tim barrel]]
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Current revision

Crystal Structure of Kemp Elimination Catalyst 1A53-2

PDB ID 3nyz

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