3TP4

Crystal Structure of engineered protein at the resolution 1.98A, Northeast Structural Genomics Consortium Target OR128

Summary for 3TP4

• Entry DOI: 10.2210/pdb3tp4/pdb
• Related: 2BVY
• Descriptor: computational Design of Enzyme, ACETIC ACID, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: structural genomics, psi-biology, protein structure initiative, northeast structural genomics consortium, nesg, or128, osh97, unknown function
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 100611.08

Authors

Kuzin, A.,Su, M.,Seetharaman, J.,Rajagopalan, S.,Everett, J.K.,Nair, R.,Acton, T.B.,Rost, B.,Baker, D.,Montelione, G.T.,Hunt, J.F.,Tong, L.,Northeast Structural Genomics Consortium (NESG) (deposition date: 2011-09-07, release date: 2011-10-05, Last modification date: 2023-12-06)

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

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: 24705591
DOI: 10.1038/nchembio.1498

Experimental method

X-RAY DIFFRACTION (1.979 Å)