1NJ9

Cocaine hydrolytic antibody 15A10

DOI: 10.2210/pdb1NJ9/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2002-12-30 Released: 2004-02-17
Deposition Author(s): Larsen, N.A., de Prada, P., Deng, S.X., Zhu, X., Landry, D.W., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.283
R-Value Work: 0.199
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystallographic and biochemical analysis of cocaine-degrading antibody 15A10.

Larsen, N.A., de Prada, P., Deng, S.X., Mittal, A., Braskett, M., Zhu, X., Wilson, I.A., Landry, D.W.

(2004) Biochemistry 43: 8067-8076

PubMed: 15209502 Search on PubMed
DOI: 10.1021/bi049495l
Primary Citation of Related Structures:
1NJ9

PubMed Abstract:

Catalytic antibody 15A10 hydrolyzes the benzoyl ester of cocaine to form the nonpsychoactive metabolites benzoic acid and ecgonine methylester. Here, we report biochemical and structural studies that characterize the catalytic mechanism. The crystal structure of the cocaine-hydrolyzing monoclonal antibody (mAb) 15A10 has been determined at 2.35 A resolution. The binding pocket is fairly shallow and mainly hydrophobic but with a cluster of three hydrogen-bond donating residues (TrpL96, AsnH33, and TyrH35). Computational docking of the transition state analogue (TSA) indicates that these residues are appropriately positioned to coordinate the phosphonate moiety of the TSA and, hence, form an oxyanion hole. Tyrosine modification of the antibody with tetranitromethane reduced hydrolytic activity to background level. The contribution from these and other residues to catalysis and TSA binding was explored by site-directed mutagenesis of 15A10 expressed in a single chain fragment variable (scFv) format. The TyrH35Phe mutant had 4-fold reduced activity, and TrpL96Ala, TrpL96His, and AsnH33Ala mutants were all inactive. Comparison with an esterolytic antibody D2.3 revealed a similar arrangement of tryptophan, asparagine, and tyrosine residues in the oxyanion hole that stabilizes the transition state for ester hydrolysis. Furthermore, the crystal structure of the bacterial cocaine esterase (cocE) also showed that the cocE employs a tyrosine hydroxyl in the oxyanion hole. Thus, the biochemical and structural data are consistent with the catalytic antibody providing oxyanion stabilization as its major contribution to catalysis.

Related Citations:

Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal.
Larsen, N.A., Heine, A., de Prada, P., Redwan, E.R., Yeates, T.O., Landry, D.W., Wilson, I.A.
(2002) Acta Crystallogr D Biol Crystallogr 58: 2055

Organizational Affiliation:

The Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin variable chain	A, L	212	Mus musculus	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin heavy chain	B, H	215	Mus musculus	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [L] SDF format, chain F [L] SDF format, chain G [H] SDF format, chain H [H] SDF format, chain I [H] SDF format, chain J [A] SDF format, chain K [B] SDF format, chain L [B] MOL2 format, chain E [L] MOL2 format, chain F [L] MOL2 format, chain G [H] MOL2 format, chain H [H] MOL2 format, chain I [H] MOL2 format, chain J [A] MOL2 format, chain K [B] MOL2 format, chain L [B]	A, B, H, L	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction