PDBsum entry 2gfb

Immunoglobulin

PDB id: 2gfb

Contents

Protein chains

(+ 2 more) 214 a.a. *

(+ 2 more) 219 a.a. *

* Residue conservation analysis

PDB id:

2gfb

Name:

Immunoglobulin

Title:

Crystal structure of a catalytic fab having esterase-like activity

Structure:

Igg2a cnj206 fab (light chain). Chain: a, c, e, g, i, k, m, o. Igg2a cnj206 fab (heavy chain). Chain: b, d, f, h, j, l, n, p

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.213

Authors:

B.Golinelli-Pimpaneau,M.Knossow

Key ref:

B.Golinelli-Pimpaneau et al. (1994). Crystal structure of a catalytic antibody Fab with esterase-like activity. Structure, 2, 175-183. PubMed id: 8069632 DOI: 10.1016/S0969-2126(00)00019-8

Date:

07-Jul-94 Release date: 30-Sep-94

Protein chains

No UniProt id for this chain

Struc: 214 a.a.

Protein chains

No UniProt id for this chain

Struc: 219 a.a.

DOI no: 10.1016/S0969-2126(00)00019-8

Structure 2:175-183 (1994)

PubMed id: 8069632

Crystal structure of a catalytic antibody Fab with esterase-like activity.

B.Golinelli-Pimpaneau, B.Gigant, T.Bizebard, J.Navaza, P.Saludjian, R.Zemel, D.S.Tawfik, Z.Eshhar, B.S.Green, M.Knossow.

ABSTRACT

BACKGROUND: Antibodies with catalytic properties can be prepared by eliciting an antibody response against 'transition state analog' haptens. The specificity, rate and number of reaction cycles observed with these antibodies more closely resemble the properties of enzymes than any of the many other known enzyme-mimicking systems. RESULTS: We have determined to 3 A resolution the first X-ray structure of a catalytic antibody Fab. This antibody catalyzes the hydrolysis of a p-nitrophenyl ester. In conjunction with binding studies in solution, this structure of the uncomplexed site suggests a model for transition state fixation where two tyrosines mimic the oxyanion binding hole of serine proteases. A comparison with the structures of known Fabs specific for low molecular weight haptens reveals that this catalytic antibody has an unusually long groove at its combining site. CONCLUSION: Since transition state analogs contain elements of the desired product, product inhibition is a severe problem in antibody catalysis. The observation of a long groove at the combining site may relate to the ability of this catalytic antibody to achieve multiple cycles of reaction.

Selected figure(s)

Figure 1.
Figure 1. Diagrams of the hydrolysis reaction catalyzed by CNJ206 and of the compounds used in this study. 1 is the substrate (a p- nitrophenyl ester); 2 is the transition state analog (TSA) hapten used to elicit CNJ206; 3 is a short TSA used to select catalytic antibodies; 4 and 5 were used in binding studies with CNJ206. Figure 1. Diagrams of the hydrolysis reaction catalyzed by CNJ206 and of the compounds used in this study. 1 is the substrate (a p- nitrophenyl ester); 2 is the transition state analog (TSA) hapten used to elicit CNJ206; 3 is a short TSA used to select catalytic antibodies; 4 and 5 were used in binding studies with CNJ206.

Figure 5.
Figure 5. Model of the transition-state analog bound to CNJ206. (a) The same view as in Figure 2, illustrating a model of p-nitrophenyl methylphosphonate (compound 3 of Figure 1) bound to CNJ206. The inhibitor 3 was modeled using SYBYL (Molecular Modeling Software, Tripos Associates, St Louis, MO) and structural data [43] and adjusted into the binding site of CNJ206 using FRODO [44]. Atomic positions were then subjected to energy refinement with X-PLOR [41]. Atoms further than 9 å from the hapten were kept fixed, while soft harmonic constraints were applied to atoms in a shell between 7 and 9 å from the hapten. For residues within 7 å of the hapten, softer constraints were applied to main-chain atoms, while side chains were left unconstrained. Polar or charged residues lining the cavity are labeled. The intramolecular salt link between Arg L46 and Asp L55, which stabilizes the conformation of the arginine is shown. The orientation presented allows hydrogen bonds (dotted lines) to be made both to the nitro group and to the methyl phosphonate (atom colours as described for Figure 4). (b)A space-filling representation of the same model. The phosphorous atom is shown here in green with the phenyl ring and methyl group of compound 3 in yellow. In this orientation, compound 3 buries 242 å ^2of surface, which is 71 % of its total accessible surface area (calculated using a 1.4 å radius probe). Figure 5. Model of the transition-state analog bound to CNJ206. (a) The same view as in [3]Figure 2, illustrating a model of p-nitrophenyl methylphosphonate (compound 3 of [4]Figure 1) bound to CNJ206. The inhibitor 3 was modeled using SYBYL (Molecular Modeling Software, Tripos Associates, St Louis, MO) and structural data [[5]43] and adjusted into the binding site of CNJ206 using FRODO [[6]44]. Atomic positions were then subjected to energy refinement with X-PLOR [[7]41]. Atoms further than 9 å from the hapten were kept fixed, while soft harmonic constraints were applied to atoms in a shell between 7 and 9 å from the hapten. For residues within 7 å of the hapten, softer constraints were applied to main-chain atoms, while side chains were left unconstrained. Polar or charged residues lining the cavity are labeled. The intramolecular salt link between Arg L46 and Asp L55, which stabilizes the conformation of the arginine is shown. The orientation presented allows hydrogen bonds (dotted lines) to be made both to the nitro group and to the methyl phosphonate (atom colours as described for [8]Figure 4). (b)A space-filling representation of the same model. The phosphorous atom is shown here in green with the phenyl ring and methyl group of compound 3 in yellow. In this orientation, compound 3 buries 242 å ^2of surface, which is 71 % of its total accessible surface area (calculated using a 1.4 å radius probe).

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 175-183) copyright 1994.

Figures were selected by an automated process.