5XQW

Catalytic antibody 7B9

Summary for 5XQW

• Entry DOI: 10.2210/pdb5xqw/pdb
• Descriptor: Fab fragment of catalytic antibody 7B9, light chain, Fab fragment of catalytic antibody 7B9, heavy chain, ethyl-[(4-nitrophenyl)methoxy]phosphinic acid, ... (4 entities in total)
• Functional Keywords: catalytic antibody, hydrolytic enzyme, fab, transition-state analogue, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 2
• Total formula weight: 46792.72

Authors

Ito, N.,Fujii, I.,Tsumuraya, T. (deposition date: 2017-06-07, release date: 2018-04-18, Last modification date: 2024-11-06)

Primary citation

Miyamoto, N.,Yoshimura, M.,Okubo, Y.,Suzuki-Nagata, K.,Tsumuraya, T.,Ito, N.,Fujii, I.
Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters.
Bioorg. Med. Chem., 26:1412-1417, 2018

PubMed Abstract: Catalytic antibody 7B9, which was elicited against p-nitrobenzyl phosphonate transition-state analogue (TSA) 1, hydrolyzes a wide range of p-nitrobenzyl monoesters and thus shows broad substrate tolerance. To reveal the molecular basis of this substrate tolerance, the 7B9 Fab fragment complexed with p-nitrobenzyl ethylphosphonate 2 was crystallized and the three-dimensional structure was determined. The crystal structure showed that the strongly antigenic p-nitrobenzyl moiety occupied a relatively shallow antigen-combining site and therefore the alkyl moiety was located outside the pocket. These results support the observed broad substrate tolerance of 7B9 and help rationalize how 7B9 can catalyze various p-nitrobenzyl ester derivatives. The crystal structure also showed that three amino acid residues (Asn, Ser, and Arg) were placed in key positions to form hydrogen bonds with the phosphonate oxygens of the transitions-state analogue. In addition, the role of these amino acid residues was examined by site-directed mutagenesis to alanine: all mutants (AsnAla, SerAla, and ArgAla) showed no detectable catalytic activity. Coupling the findings from our structural studies with these mutagenesis results clarified the structural basis of the observed broad substrate tolerance of antibody 7B9-catalyzed hydrolyses. Our findings provide new strategies for the generation of catalytic antibodies that accept a broad range of substrates, aiding their practical application in synthetic organic chemistry.

PubMed: 29496413
DOI: 10.1016/j.bmc.2017.07.050

Experimental method

X-RAY DIFFRACTION (2.2 Å)