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| | ==Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63.== | | ==Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63.== |
| - | <StructureSection load='3tc6' size='340' side='right' caption='[[3tc6]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='3tc6' size='340' side='right'caption='[[3tc6]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3tc6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TC6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3tc6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TC6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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]] 1.6Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trpC, SSO0895 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </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=3tc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tc6 OCA], [https://pdbe.org/3tc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tc6 RCSB], [https://www.ebi.ac.uk/pdbsum/3tc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tc6 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tc6 OCA], [http://pdbe.org/3tc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tc6 RCSB], [http://www.ebi.ac.uk/pdbsum/3tc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tc6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/TRPC_SACS2 TRPC_SACS2] |
| - | Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of beta-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10-3s-1) and kcat/KM (11-25M-1s-1) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >105-fold rate accelerations that were achieved are within 1-3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat=106 to 108) and an extensively evolved computational design (kcat/kuncat>107). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches.
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| - | Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design.,Bjelic S, Kipnis Y, Wang L, Pianowski Z, Vorobiev S, Su M, Seetharaman J, Xiao R, Kornhaber G, Hunt JF, Tong L, Hilvert D, Baker D J Mol Biol. 2013 Oct 23. pii: S0022-2836(13)00655-4. doi:, 10.1016/j.jmb.2013.10.012. PMID:24161950<ref>PMID:24161950</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
| + | |
| - | <div class="pdbe-citations 3tc6" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Indole-3-glycerol phosphate synthase|Indole-3-glycerol phosphate synthase]] | + | *[[IGPS 3D structures|IGPS 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Indole-3-glycerol-phosphate synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Sulso]] | + | [[Category: Saccharolobus solfataricus P2]] |
| - | [[Category: Acton, T B]] | + | [[Category: Acton TB]] |
| - | [[Category: Baker, D]] | + | [[Category: Baker D]] |
| - | [[Category: Bjelic, S]] | + | [[Category: Bjelic S]] |
| - | [[Category: Ciccosanti, C]] | + | [[Category: Ciccosanti C]] |
| - | [[Category: Everett, J K]] | + | [[Category: Everett JK]] |
| - | [[Category: Hunt, J F]] | + | [[Category: Hunt JF]] |
| - | [[Category: Kipnis, Y]] | + | [[Category: Kipnis Y]] |
| - | [[Category: Montelione, G T]] | + | [[Category: Montelione GT]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Sahdev S]] |
| - | [[Category: Sahdev, S]] | + | [[Category: Seetharaman J]] |
| - | [[Category: Seetharaman, J]] | + | [[Category: Su M]] |
| - | [[Category: Su, M]] | + | [[Category: Tong L]] |
| - | [[Category: Tong, L]] | + | [[Category: Vorobiev S]] |
| - | [[Category: Vorobiev, S]] | + | [[Category: Wang L]] |
| - | [[Category: Wang, L]] | + | [[Category: Xiao R]] |
| - | [[Category: Xiao, R]] | + | |
| - | [[Category: Engineered protein]]
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| - | [[Category: Lyase]]
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| - | [[Category: Nesg]]
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| - | [[Category: Or63]]
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| - | [[Category: Psi-biology]]
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