3v45: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3v45]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V45 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V45 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3v45]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V45 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V45 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dx6|2dx6]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=3v45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v45 OCA], [https://pdbe.org/3v45 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v45 RCSB], [https://www.ebi.ac.uk/pdbsum/3v45 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v45 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=3v45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v45 OCA], [https://pdbe.org/3v45 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v45 RCSB], [https://www.ebi.ac.uk/pdbsum/3v45 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v45 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.
Design of activated serine-containing catalytic triads with atomic-level accuracy.,Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D Nat Chem Biol. 2014 Apr 6. doi: 10.1038/nchembio.1498. PMID:24705591<ref>PMID:24705591</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3v45" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Acton, T B]]
[[Category: Acton TB]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Everett, J K]]
[[Category: Everett JK]]
[[Category: Hunt, J F]]
[[Category: Hunt JF]]
[[Category: Kohan, E]]
[[Category: Kohan E]]
[[Category: Kuzin, A]]
[[Category: Kuzin A]]
[[Category: Maglaqui, M]]
[[Category: Maglaqui M]]
[[Category: Montelione, G T]]
[[Category: Montelione GT]]
[[Category: Structural genomic]]
[[Category: Nair R]]
[[Category: Nair, R]]
[[Category: Rajagopalan S]]
[[Category: Rajagopalan, S]]
[[Category: Rost B]]
[[Category: Rost, B]]
[[Category: Seetharaman J]]
[[Category: Seetharaman, J]]
[[Category: Su M]]
[[Category: Su, M]]
[[Category: Tong L]]
[[Category: Tong, L]]
[[Category: Xiao R]]
[[Category: Xiao, R]]
[[Category: De novo design]]
[[Category: De novo protein]]
[[Category: Nesg]]
[[Category: PSI, Protein structure initiative]]
[[Category: Psi-biology]]
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