3CFK

Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form

Summary for 3CFK

• Entry DOI: 10.2210/pdb3cfk/pdb
• Related: 1Y0L 1Y18 3CFJ
• Descriptor: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein, CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein, CADMIUM ION, ... (6 entities in total)
• Functional Keywords: immunoglobulin, catalytic antibody, chimeric fab, apo form, proton transfer, conformational change, immune system, chimera, immunoglobulin domain, immunoglobulin v region
• Biological source: Mus musculus (mouse); More
• Total number of polymer chains: 16
• Total formula weight: 387019.43

Authors

Debler, E.W.,Wilson, I.A. (deposition date: 2008-03-04, release date: 2008-04-15, Last modification date: 2024-10-30)

Primary citation

Debler, E.W.,Muller, R.,Hilvert, D.,Wilson, I.A.
Conformational isomerism can limit antibody catalysis.
J.Biol.Chem., 283:16554-16560, 2008

PubMed Abstract: Ligand binding to enzymes and antibodies is often accompanied by protein conformational changes. Although such structural adjustments may be conducive to enzyme catalysis, much less is known about their effect on reactions promoted by engineered catalytic antibodies. Crystallographic and pre-steady state kinetic analyses of antibody 34E4, which efficiently promotes the conversion of benzisoxazoles to salicylonitriles, show that the resting catalyst adopts two interconverting active-site conformations, only one of which is competent to bind substrate. In the predominant isomer, the indole side chain of Trp(L91) occupies the binding site and blocks ligand access. Slow conformational isomerization of this residue, on the same time scale as catalytic turnover, creates a deep and narrow binding site that can accommodate substrate and promote proton transfer using Glu(H50) as a carboxylate base. Although 34E4 is among the best catalysts for the deprotonation of benzisoxazoles, its efficiency appears to be significantly limited by this conformational plasticity of its active site. Future efforts to improve this antibody might profitably focus on stabilizing the active conformation of the catalyst. Analogous strategies may also be relevant to other engineered proteins that are limited by an unfavorable conformational pre-equilibrium.

PubMed: 18417480
DOI: 10.1074/jbc.M710256200

Experimental method

X-RAY DIFFRACTION (2.6 Å)