PDBsum entry 1yeh

Catalytic antibody

PDB id: 1yeh

Contents

Protein chains

219 a.a.

222 a.a. *

Metals

_ZN ×7

Waters ×130

* Residue conservation analysis

PDB id:

1yeh

Name:

Catalytic antibody

Title:

Structure of igg2a fab fragment

Structure:

Fab fragment. Chain: l. Other_details: ig gamma-2a chain c region (d2.3). Fab fragment. Chain: h. Other_details: ig gamma-2a chain c region (d2.3)

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

2.55Å R-factor: 0.181 R-free: 0.231

Authors:

B.Gigant,M.Knossow

Key ref:

B.Gigant et al. (1997). X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release. Proc Natl Acad Sci U S A, 94, 7857-7861. PubMed id: 9223277 DOI: 10.1073/pnas.94.15.7857

Date:

29-May-97 Release date: 03-Dec-97

Protein chain

No UniProt id for this chain

Struc: 219 a.a.

Protein chain

P01863  (GCAA_MOUSE) -  Ig gamma-2A chain C region, A allele from Mus musculus

Seq: 330 a.a.

Struc: 222 a.a.

DOI no: 10.1073/pnas.94.15.7857

Proc Natl Acad Sci U S A 94:7857-7861 (1997)

PubMed id: 9223277

X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release.

B.Gigant, J.B.Charbonnier, Z.Eshhar, B.S.Green, M.Knossow.

ABSTRACT

The x-ray structures of the unliganded esterase-like catalytic antibody D2.3 and its complexes with a substrate analogue and with one of the reaction products are analyzed. Together with the structure of the phosphonate transition state analogue hapten complex, these crystal structures provide a complete description of the reaction pathway. At alkaline pH, D2.3 acts by preferential stabilization of the negatively charged oxyanion intermediate of the reaction that results from hydroxide attack on the substrate. A tyrosine residue plays a crucial role in catalysis: it activates the ester substrate and, together with an asparagine, it stabilizes the oxyanion intermediate. A canal allows facile diffusion of water molecules to the reaction center that is deeply buried in the structure. Residues bordering this canal provide targets for mutagenesis to introduce a general base in the vicinity of the reaction center.

Selected figure(s)

Figure 1.
Fig. 1. Chemical reaction catalyzed by D2.3 and structures of the compounds used in this study. Ester 1 is a substrate hydrolyzed^ by D2.3. Crystal structures examined are those of complexes of^ D2.3 with p-nitrobenzyl alcohol 2 (one of the products of the hydrolysis of 1), p-nitrobenzyl phosphonate 3^ (the TSA hapten used to elicit D2.3), and p-nitrobenzyl amide^ 4, a stable analogue of the substrate ester 1.

Figure 2.
Fig. 2. Schematic views of D2.3 Fab residues that interact with the ligands examined. Residue numbering is according to ref. 24. In A-C, the ligands are in blue, the C[ ]trace of the Fab is in green, and water molecules are in red. Hydrogen bonds are shown as dotted lines. (A) Complex of D2.3 with amide 4, a stable^ SA. (B) Complex of D2.3 with TSA 3. (C) Complex of D2.3^ with the reaction product 2, p-nitrobenzyl alcohol. Electron density corresponding to an acetate molecule was located in the^ combing site. The acetate is in yellow; the oxygens and the methyl of the acetate were distinguished on the basis of the hydrogen bonds established. A-C were drawn with MOLSCRIPT (25). (D) View of the canal (D2.3-4 structure) that allows water diffusion to the carbon atom of the carbonyl of 4 analogous to the^ reaction center in the complex of D2.3 with 1. The surface^ accessible to the exterior of a water molecule represented by a 1.4-Å radius sphere is cut to show the canal; its face toward^ the complexed Fab atoms is in blue, and the one facing the exterior is in white. Only the residues that border the canal are represented. Ligand 4 is in green; the water molecule (magenta) closest to the analogue of the reaction center is within hydrogen bonding distance and angle to Arg-H50 (hydrogen bond not shown). Nitrogen N 1 of His-H35 makes a hydrogen bond to Trp-H47 (not shown) that is conserved in antibodies; therefore, the N 2 nitrogen of His-H35^ (which is part of the canal's wall) is protonated, and His-H35^ most likely does not function as a general base in the hydrolysis catalyzed by D2.3. D was rendered in the AVS environment (26).