Structural basis for a disfavored elimination reaction in catalytic antibody 1D4.
Murine antibody 1D4 selectively catalyzes a highly disfavored beta-elimination reaction. Crystal structures of unliganded 1D4 and 1D4 in complex with a transition-state analog (TSA) have elucidated a possible general base mode of catalysis. The structures of the unliganded and liganded Fabs were determined to 1.80 and 1.85 A resolution, respectively. The structure of the complex reveals a binding pocket with high shape complementarity to the TSA, which is recruited to coerce the substrate into the sterically demanding, eclipsed conformation that is required for catalysis. A histidine residue and two water molecules are likely involved in the catalysis. The structure supports either a concerted E2 or stepwise E1cB-like mechanism for elimination. Finally, the liganded 1D4 structure shows minor conformational rearrangements in CDR H2, indicative of induced-fit binding of the hapten. 1D4 has pushed the boundaries of antibody-mediated catalysis into the realm of disfavored reactions and, hence, represents an important milestone in the development of this technology.
Larsen
N A
NA
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA.
Heine
A
A
Crane
L
L
Cravatt
B F
BF
Lerner
R A
RA
Wilson
I A
IA
D000818:Animals; D017151:Antibodies, Catalytic / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism*; D001666:Binding Sites, Antibody; D002384:Catalysis; D002412:Cations / Q000378:metabolism; D018360:Crystallography, X-Ray; D019277:Entropy; D006241:Haptens / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D006860:Hydrogen Bonding; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism*; D007074:Immunoglobulin G / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D008024:Ligands; D051379:Mice; D008958:Models, Molecular; D011487:Protein Conformation; D012997:Solvents; D055672:Static Electricity; D013329:Structure-Activity Relationship
D017151:Antibodies, Catalytic; D002412:Cations; D006241:Haptens; D007140:Immunoglobulin Fab Fragments; D007074:Immunoglobulin G; D008024:Ligands; D012997:Solvents