PDBsum entry 1kno

Catalytic antibody

PDB id: 1kno

Contents

Protein chains

214 a.a. *

220 a.a. *

Ligands

PNP ×3

Metals

_ZN

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the complex of a catalytic antibody FAB fragment with a transition state analog: structural similarities in esterase-Like catalytic antibodies.

Authors

J.B.Charbonnier, E.Carpenter, B.Gigant, B.Golinelli-Pimpaneau, Z.Eshhar, B.S.Green, M.Knossow.

Ref.

Proc Natl Acad Sci U S A, 1995, 92, 11721-11725. [DOI no: 10.1073/pnas.92.25.11721]

PubMed id

8524836

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 83%.

Abstract

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.

Secondary reference #1

Title

Differences in the biochemical properties of esterolytic antibodies correlate with structural diversity.

Authors

R.Zemel, D.G.Schindler, D.S.Tawfik, Z.Eshhar, B.S.Green.

Ref.

Mol Immunol, 1994, 31, 127-137. [DOI no: 10.1016/0161-5890(94)90085-X]

PubMed id

8309476

Secondary reference #2

Title

Crystal structure of a catalytic antibody FAB with esterase-Like activity.

Authors

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

Ref.

Structure, 1994, 2, 175-183. [DOI no: 10.1016/S0969-2126(00)00019-8]

PubMed id

8069632

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 reproduced from the cited reference with permission from Cell Press