PDBsum entry 1lo2

Immune system

PDB id: 1lo2

Contents

Protein chains

219 a.a. *

220 a.a. *

Ligands

OX1 ×2

Waters ×140

* Residue conservation analysis

PDB id:

1lo2

Name:

Immune system

Title:

Retro-diels-alderase catalytic antibody

Structure:

If kappa light chain. Chain: x, l. Fragment: fab fragment. Synonym: catalytic antibody 9d9. Ig gamma 2a heavy chain. Chain: y, h

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Other_details: the antibodies were isolated from hybridoma cells and fab fragments were generated by papain digestion.. Fab fragments were generated by papain digestion.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.210 R-free: 0.248

Authors:

M.Hugot,J.L.Reymond,U.Baumann

Key ref:

M.Hugot et al. (2002). A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue. Proc Natl Acad Sci U S A, 99, 9674-9678. PubMed id: 12093912 DOI: 10.1073/pnas.142286599

Date:

06-May-02 Release date: 26-Jun-02

Protein chains

Q65ZC0  (Q65ZC0_MOUSE) -  Kappa light chain C_region (Fragment) from Mus musculus

Seq: 219 a.a.

Struc: 219 a.a.*

Protein chains

Q91Z05  (Q91Z05_MOUSE) -  Ighg protein from Mus musculus

Seq: 473 a.a.

Struc: 220 a.a.*

* PDB and UniProt seqs differ at 75 residue positions (black crosses)

DOI no: 10.1073/pnas.142286599

Proc Natl Acad Sci U S A 99:9674-9678 (2002)

PubMed id: 12093912

A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue.

M.Hugot, N.Bensel, M.Vogel, M.T.Reymond, B.Stadler, J.L.Reymond, U.Baumann.

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.

Selected figure(s)

Figure 1.
Fig. 1. Reaction scheme and haptens used in this study. The retro-Diels-Alder reaction of pro-drug 1a (k[un] = 9.8 10^ 6 s 1 conditions: 31°C in PBS pH 7.4, 10% vol/vol dimethylformamide) releases nitroxyl and anthracene 2a. The reaction is catalyzed by antibodies 9D9 (anti-3), 10F11 (anti-5), and 27C5 (anti-3,4). The reaction with the regioisomeric substrate 1b (k[un] = 7.1 10^ 6 s 1) is also catalyzed weakly by the antibodies. The unreactive substrate analog 6 and product analogue 2b were used for crystallization. Substrate analogue 1c and product analog 2c and transition state model 7 were used for docking studies.

Figure 3.
Fig. 3. Active site of the abzyme. (Left) 10F11 in complex with OXY (compound 6). The hydrogen bonding network is shown as dotted lines. (Right) Surface representation of the binding pocket of Fab 10F11 with the transition state analogue BCN (compound 4) of the retro-Diels-Alder reaction. View is from the top of the binding site showing the fit of the ligand BCN. The light pink transparent surface represents V[L] and the light blue transparent surface represents V[H]. Note the presence of water molecules inside the pocket. Figure prepared with DINO (http://www.dino3d.org).

Figures were selected by an automated process.