Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.
The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.
Charbonnier
J B
JB
Laboratoire de Biologie Structurale, Centre National de la Recherche Scientifique, Université Paris Sud, Gif-sur-Yvette, France.
Carpenter
E
E
Gigant
B
B
Golinelli-Pimpaneau
B
B
Eshhar
Z
Z
Green
B S
BS
Knossow
M
M
D017151:Antibodies, Catalytic / Q000737:chemistry* / Q000378:metabolism; D000911:Antibodies, Monoclonal / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D003461:Crystallography; D004950:Esterases / Q000737:chemistry* / Q000378:metabolism; D006241:Haptens / Q000737:chemistry / Q000378:metabolism; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D009596:Nitrophenols / Q000737:chemistry / Q000276:immunology; D011487:Protein Conformation; D013379:Substrate Specificity; D017356:Synchrotrons
D017151:Antibodies, Catalytic; D000911:Antibodies, Monoclonal; D006241:Haptens; D007140:Immunoglobulin Fab Fragments; D009596:Nitrophenols; D004950:Esterases; C024836:4-nitrophenol