PDBsum entry 1dzb

Immune system

PDB id: 1dzb

Contents

Protein chains

224 a.a. *

129 a.a. *

Waters ×260

* Residue conservation analysis

PDB id:

1dzb

Name:

Immune system

Title:

Crystal structure of phage library-derived single-chain fv fragment 1f9 in complex with turkey egg-white lysozyme

Structure:

Scfv fragment 1f9. Chain: a, b. Fragment: see remark 400. Turkey egg-white lysozymE C. Chain: x, y. Synonym: 1,4-beta-n-acetylmuramidasE C. Ec: 3.2.1.17

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Meleagris gallopavo. Common turkey. Organism_taxid: 9103

Biol. unit:

Hetero-Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.225 R-free: 0.306

Authors:

J.Ay,T.Keitel,G.Kuettner,H.Wessner,C.Scholz,M.Hahn,W.Hoehne

Key ref:

J.Aÿ et al. (2000). Crystal structure of a phage library-derived single-chain Fv fragment complexed with turkey egg-white lysozyme at 2.0 A resolution. J Mol Biol, 301, 239-246. PubMed id: 10926506 DOI: 10.1006/jmbi.2000.3971

Date:

23-Feb-00 Release date: 02-Nov-00

Protein chains

No UniProt id for this chain

Struc: 224 a.a.

Protein chains

P00703  (LYSC_MELGA) -  Lysozyme C from Meleagris gallopavo

Seq: 147 a.a.

Struc: 129 a.a.

Enzyme reactions

• Enzyme class: Chains X, Y: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

DOI no: 10.1006/jmbi.2000.3971

J Mol Biol 301:239-246 (2000)

PubMed id: 10926506

Crystal structure of a phage library-derived single-chain Fv fragment complexed with turkey egg-white lysozyme at 2.0 A resolution.

J.Aÿ, T.Keitel, G.Küttner, H.Wessner, C.Scholz, M.Hahn, W.Höhne.

ABSTRACT

The three-dimensional structure of the single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme (TEL) has been determined to a nominal resolution of 2.0 A by X-ray diffraction. The scFv fragment 1F9 was derived from phage-display libraries in two steps and binds both hen and turkey egg-white lysozyme, although the level of binding affinity is two orders of magnitude greater for the turkey lysozyme. The comparison of the crystal structure with a model of the single-chain Fv fragment 1F9 in complex with hen egg-white lysozyme (HEL) reveals that in the latter a clash between Asp101 in lysozyme and Trp98 of the complementarity determining region H3 of the heavy chain variable domain occurs. This is the only explanation apparent from the crystal structure for the better binding of TEL compared to HEL.The binding site topology on the paratope is not simply a planar surface as is usually found in antibody-protein interfaces, but includes a cleft between the light chain variable domain and heavy chain variable domain large enough to accommodate a loop from the lysozyme. The scFv fragment 1F9 recognizes an epitope on TEL that differs from the three antigenic determinants recognized in other known crystal structures of monoclonal antibodies in complex with lysozyme.

Selected figure(s)

Figure 1.
Figure 1. (a) Stereo surface representation of the 1F9/TEL complex. The V[H] domain is orange, the V[L] domain is gray and TEL, which is separated by 10 Å for better clarity of the contact surface is shown in red. The residues indicated in blue are involved in the antigen-antibody interaction (Table 2). The representation was drawn with WebLab ViewerPro [Molecular Simulation 1999]. The buried solvent-accessible surface area calculated with the program AREAIMOL [Collaborative Computational Project 1994]. (b) Stereo-view of the tube a-carbon trace of 1F9/TEL complex. The CDR regions of the V[H] domain are shown yellow, and the CDR regions of the V[L] domain are shown light gray. TEL is least-squares superimposed with the uncomplexed TEL (PDB entry 135L, [Harata 1993]) in light blue and uncomplexed HEL (PDB entry 1AKI, [Artymiuk et al 1982]) in blue calculated by the program LSQKAB [Collaborative Computational Project 1994]. This and the following presentation are drawn with SETOR [Evans 1993]. (c) Stereo-view of the interaction region with the side-chain contacts of the lysozyme residue 101 (Gly in TEL, Asp in HEL) with CDR L1 and H3. Hydrogen bonds are marked in black.

Figure 2.
Figure 2. Least-squares superposition of four lysozyme crystal structures in complex with their respective antibody Fv fragments: scFv 1F9 in red, Fv D1.3 in blue (PDB entry 1VFB, [Bhat et al 1994]), Fv fragment of HyHEL-5 Fab in orange (PDB entry 3HFL, [Cohen et al 1996]) and Fv fragment of HyHEL-10 Fab in light blue (PDB entry 3HFM, [Padlan et al 1989]). This antibody-antigen complexes, shown as stereographic a-carbon traces generated by SETOR [Evans 1993], are examples for the three different epitope regions on lysozyme described in crystal structures. The disulfide bridges are drawn in yellow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 239-246) copyright 2000.