1LO4

Retro-Diels-Alderase Catalytic antibody 9D9

Summary for 1LO4

• Entry DOI: 10.2210/pdb1lo4/pdb
• Related: 1L00 1L02 1L03
• Descriptor: If kappa light chain, Ig gamma 2a heavy chain (3 entities in total)
• Functional Keywords: fab, catalytic antibody, retro-deils-alderase, immune system
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 2
• Total formula weight: 47651.33

Authors

Hugot, M.,Reymond, J.L.,Baumann, U. (deposition date: 2002-05-06, release date: 2002-07-03, Last modification date: 2024-11-20)

Primary citation

Hugot, M.,Bensel, N.,Vogel, M.,Reymond, M.T.,Stadler, B.,Reymond, J.L.,Baumann, U.
A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue.
Proc.Natl.Acad.Sci.USA, 99:9674-9678, 2002

PubMed Abstract: The nitroxyl synthase catalytic antibodies 10F11, 9D9, and 27C5 catalyze the release of nitroxyl from a bicyclic pro-drug by accelerating a retro-Diels-Alder reaction. The Fabs (antigen-binding fragments) of these three catalytic antibodies were cloned and sequenced. Fab 9D9 was crystallized in the apo-form and in complex with one transition state analogue of the reaction. Crystal structures of Fab 10F11 in complex with ligands mimicking substrate, transition state, and product have been determined at resolutions ranging from 1.8 to 2.3 A. Antibodies 9D9 and 10F11 show increased shape complementarity (as quantified by the program sc) to the hapten and to a modeled transition state as compared with substrate and product. The shape complementarity is mediated to a large extent by an aromatic residue (tyrosine or tryptophan) at the bottom of the hydrophobic active pocket, which undergoes pi-stacking interactions with the aromatic rings of the ligands. Another factor contributing to the different reactivity of the regioisomers probably arises because of hydrogen-bonding interactions between the nitroxyl bridge and the backbone amide of PheH101 and possibly a conserved water molecule.

PubMed: 12093912
DOI: 10.1073/pnas.142286599

Experimental method

X-RAY DIFFRACTION (2.4 Å)