PDBsum entry 4jvv

Structural genomics, unknown function

PDB id: 4jvv

Contents

Protein chain

158 a.a.

Waters ×93

PDB id:

4jvv

Name:

Structural genomics, unknown function

Title:

Crystal structure of the evolved variant of the computationally designed serine hydrolase, osh55.4_h1, covalently bound with diisopropyl fluorophosphate (dfp), northeast structural genomics consortium (nesg) target or273

Structure:

Evolved variant of the computationally designed serine hydrolase. Chain: a. Engineered: yes

Source:

Synthetic construct. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_cell_line: bl21(de3) + magic.

Resolution:

2.29Å R-factor: 0.195 R-free: 0.244

Authors:

A.Kuzin,S.Lew,S.Rajagopalan,J.Seetharaman,S.Tong,J.K.Everett, T.B.Acton,D.Baker,G.T.Montelione,L.Tong,J.F.Hunt,Northeast Structural Genomics Consortium (Nesg)

Key ref:

S.Rajagopalan et al. (2014). Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat Chem Biol, 10, 386-391. PubMed id: 24705591 DOI: 10.1038/nchembio.1498

Date:

26-Mar-13 Release date: 24-Apr-13

Protein chain

No UniProt id for this chain

Struc: 158 a.a.

DOI no: 10.1038/nchembio.1498

Nat Chem Biol 10:386-391 (2014)

PubMed id: 24705591

Design of activated serine-containing catalytic triads with atomic-level accuracy.

S.Rajagopalan, C.Wang, K.Yu, A.P.Kuzin, F.Richter, S.Lew, A.E.Miklos, M.L.Matthews, J.Seetharaman, M.Su, J.F.Hunt, B.F.Cravatt, D.Baker.

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.