3FO2 image
Deposition Date 2008-12-27
Release Date 2009-11-10
Last Version Date 2024-10-30
Entry Detail
PDB ID:
3FO2
Keywords:
Title:
Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Gln mutant)
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.18 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Catalytic antibody Fab 13G5 IgG2b heavy chain chimera
Chain IDs:B (auth: H), D (auth: B)
Chain Length:229
Number of Molecules:2
Biological Source:Mus musculus, Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Catalytic antibody Fab 13G5 kappa light chain chimera
Mutations:E39Q
Chain IDs:A (auth: L), C (auth: A)
Chain Length:219
Number of Molecules:2
Biological Source:Mus musculus, Homo sapiens
Ligand Molecules
Primary Citation
An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.
Proc.Natl.Acad.Sci.USA 106 18539 18544 (2009)
PMID: 19846764 DOI: 10.1073/pnas.0902700106

Abstact

Design of catalysts featuring multiple functional groups is a desirable, yet formidable goal. Antibody 13G5, which accelerates the cleavage of unactivated benzisoxazoles, is one of few artificial enzymes that harness an acid and a base to achieve efficient proton transfer. X-ray structures of the Fab-hapten complexes of wild-type 13G5 and active-site variants now afford detailed insights into its mechanism. The parent antibody preorganizes Asp(H35) and Glu(L34) to abstract a proton from substrate and to orient a water molecule for leaving group stabilization, respectively. Remodeling the environment of the hydrogen bond donor with a compensatory network of ordered waters, as seen in the Glu(L34) to alanine mutant, leads to an impressive 10(9)-fold rate acceleration over the nonenzymatic reaction with acetate, illustrating the utility of buried water molecules in bifunctional catalysis. Generalization of these design principles may aid in creation of catalysts for other important chemical transformations.

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Primary Citation of related structures