3V45
Crystal Structure of de novo designed serine hydrolase OSH55, Northeast Structural Genomics Consortium Target OR130
Summary for 3V45
| Entry DOI | 10.2210/pdb3v45/pdb |
| Related | 2DX6 |
| Descriptor | Serine hydrolase OSH55, CHLORIDE ION, SODIUM ION, ... (4 entities in total) |
| Functional Keywords | structural genomics, psi-biology, protein structure initiative, northeast structural genomics consortium, nesg, de novo design, de novo protein |
| Total number of polymer chains | 1 |
| Total formula weight | 17756.68 |
| Authors | Kuzin, A.,Su, M.,Seetharaman, J.,Maglaqui, M.,Xiao, R.,Kohan, E.,Rajagopalan, S.,Everett, J.K.,Nair, R.,Acton, T.B.,Rost, B.,Baker, D.,Montelione, G.T.,Tong, L.,Hunt, J.F.,Northeast Structural Genomics Consortium (NESG) (deposition date: 2011-12-14, release date: 2012-01-04, Last modification date: 2023-09-13) |
| Primary citation | Rajagopalan, S.,Wang, C.,Yu, K.,Kuzin, A.P.,Richter, F.,Lew, S.,Miklos, A.E.,Matthews, M.L.,Seetharaman, J.,Su, M.,Hunt, J.F.,Cravatt, B.F.,Baker, D. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat.Chem.Biol., 10:386-391, 2014 Cited by PubMed Abstract: 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. PubMed: 24705591DOI: 10.1038/nchembio.1498 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.6 Å) |
Structure validation
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