PDBsum entry 1f3d

Immune system

PDB id: 1f3d

Contents

Protein chains

218 a.a. *

217 a.a. *

Ligands

TPM ×2

SO4

Waters ×308

* Residue conservation analysis

PDB id:

1f3d

Name:

Immune system

Title:

Catalytic antibody 4b2 in complex with its amidinium hapten.

Structure:

Catalytic antibody 4b2. Chain: l, j. Fragment: light chain - fab fragment. Catalytic antibody 4b2. Chain: h, k. Fragment: heavy chain - fab fragment

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090

Biol. unit:

Dimer (from PQS)

Resolution:

1.87Å R-factor: 0.198 R-free: 0.218

Authors:

B.Golinelli-Pimpaneau,O.Goncalves,T.Dintinger,D.Blanchard,M.Knossow, C.Tellier

Key ref:

B.Golinelli-Pimpaneau et al. (2000). Structural evidence for a programmed general base in the active site of a catalytic antibody. Proc Natl Acad Sci U S A, 97, 9892-9895. PubMed id: 10963661 DOI: 10.1073/pnas.97.18.9892

Date:

02-Jun-00 Release date: 13-Sep-00

Protein chains

A2NHM3  (A2NHM3_MOUSE) -  If kappa light chain (Fragment) from Mus musculus

Seq: 219 a.a.

Struc: 218 a.a.*

Protein chains

No UniProt id for this chain

Struc: 217 a.a.

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

DOI no: 10.1073/pnas.97.18.9892

Proc Natl Acad Sci U S A 97:9892-9895 (2000)

PubMed id: 10963661

Structural evidence for a programmed general base in the active site of a catalytic antibody.

B.Golinelli-Pimpaneau, O.Goncalves, T.Dintinger, D.Blanchard, M.Knossow, C.Tellier.

ABSTRACT

The crystal structure of the complex of a catalytic antibody with its cationic hapten at 1.9-A resolution demonstrates that the hapten amidinium group is stabilized through an ionic pair interaction with the carboxylate of a combining-site residue. The location of this carboxylate allows it to act as a general base in an allylic rearrangement. When compared with structures of other antibody complexes in which the positive moiety of the hapten is stabilized mostly by cation-pi interactions, this structure shows that the amidinium moiety is a useful candidate to elicit a carboxylate in an antibody combining site at a predetermined location with respect to the hapten. More generally, this structure highlights the advantage of a bidentate hapten for the programmed positioning of a chemically reactive residue in an antibody through charge complementarity to the hapten.

Selected figure(s)

Figure 1.
Fig. 1. Scheme of the reaction catalyzed by antibody 4B2. 4B2 catalyzes allylic rearrangement of -cyclopent-1-en-1-yl-p-acetamidophenone 2 to -cyclopentylidien-p-acetamidophenone 4 via the enediol intermediate 3, 2-[4-(1-carboxy)propylamidobenzylamino]-3,4,5,6-tetrahydropyridinium. 1a is the hapten used to generate 4B2. The structure that was determined is that of the complex of 4B2 with 2-(4-aminobenzylamino)-3,4,5,6-tetrahydropyridinium 1b. Antibody 5C8 was generated against hapten 5a, and its x-ray structure was determined in the presence of inhibitor 5b (12).

Figure 2.
Fig. 2. (A) Schematic view of the active site of the 4B2-1b complex. The ligand is in red; water molecules are indicated as red crosses; Glu L34 is indicated in green; the other polar residues are represented in blue. The C s of residues L32-L36, L89-L97, H35-H37, and H94-H99 in hypervariable loops L1, L3, H1, and H3 are shown in yellow. The aromatic residues (Trp H47, Phe L89, Tyr L96, Tyr L32, Trp H103, and Phe L98) that have hydrophobic interactions with the hapten have been represented, except Phe L98 and Trp H103 for reasons of clarity. Nitrogen N 1 of His H35 is involved in a conserved H bond with N 1 of Trp H47. His H35 is therefore neutral but cannot play the role of a general base, because its protonated nitrogen N 2 points toward the inside of the cavity. (B) Hydrogen bonding network established with catalytic residue Glu L34. Hydrogen bonds are shown as dashed lines. A Fobs-Fcalc electron density map calculated without the amidinium ligand is superimposed on the structure. The map is contoured at the level of two standard deviations. One of the oxygens of Glu L34 is hydrogen bonded to the protonated nitrogen N 2 of His L36. This tautomeric form of His L36 is stabilized by an additional hydrogen bond between its N 1 and the NH 1 of Trp H103. Residue His L36 is therefore neutral but cannot play the role of a general base, because its unprotonated nitrogen N 1 points away from the substrate. (C) Comparison of the environment of the charge of the hapten in antibodies 5C8 (in blue) and 4B2 (in yellow). 5C8 catalyzes the disfavored cyclization of an epoxyalcohol (12). The -carbons of residues of the combining site (L32-L38, L43-L50, L86-L93, L96, L98, H32-H39, H91-H95, and H102-H104) of 5C8 have been superimposed on those of 4B2 (the rms deviation is 0.645 Å). The bottom of the active sites is formed by identical residues in both antibodies (Phe L98, Trp H47, His H35, Trp H103, and Val H37). The distance between the nitrogen of 5b of 5C8 (light green) and the carbon between the two nitrogens of 1b of 4B2 (red) is 1.05 Å. In addition to the ionic interaction with glutamate L34, the hapten amidinium charge of 4B2 is stabilized through a cation- interaction with Phe L89, which is also involved in a stacking interaction with the amidine cycle. Residues of 5C8 involved in cation- interaction with the quaternary amine of 5b are (distance to the nitrogen) Tyr L91 (4.97 Å), Trp H103 (5.59 Å), His H35 (4.55 Å), His L89 (4.96 Å), and Tyr L36 (5.39 Å). In addition, in 5C8, Asp H101 (for which there is no equivalent in 4B2 because of the short H3 loop of this antibody) and Asp H95, which are, respectively, 4 Å and 3.7 Å away from the positive charge, provide a second sphere polar environment to the quaternary amine (12). Trp H47, Val H37, and Tyr L96 are not represented for reasons of clarity.