PDBsum entry 1zdc

Igg binding domain

PDB id: 1zdc

Contents

Protein chain

35 a.a.

PDB id:

1zdc

Name:

Igg binding domain

Title:

Disulfide-stabilized mini protein a domain, z34c, nmr, 24 structures

Structure:

Stable mini protein a domain, z34c. Chain: a. Engineered: yes. Other_details: stable, two-helix, igg-binding variant of protein a

Source:

Synthetic construct. Organism_taxid: 32630

NMR struc:

24 models

Authors:

M.A.Starovasnik

Key ref:

M.A.Starovasnik et al. (1997). Structural mimicry of a native protein by a minimized binding domain. Proc Natl Acad Sci U S A, 94, 10080-10085. PubMed id: 9294166 DOI: 10.1073/pnas.94.19.10080

Date:

09-Jul-97 Release date: 17-Sep-97

Protein chain

No UniProt id for this chain

Struc: 35 a.a.

DOI no: 10.1073/pnas.94.19.10080

Proc Natl Acad Sci U S A 94:10080-10085 (1997)

PubMed id: 9294166

Structural mimicry of a native protein by a minimized binding domain.

M.A.Starovasnik, A.C.Braisted, J.A.Wells.

ABSTRACT

The affinity between molecules depends both on the nature and presentation of the contacts. Here, we observe coupling of functional and structural elements when a protein binding domain is evolved to a smaller functional mimic. Previously, a 38-residue form of the 59-residue B-domain of protein A, termed Z38, was selected by phage display. Z38 contains 13 mutations and binds IgG only 10-fold weaker than the native B-domain. We present the solution structure of Z38 and show that it adopts a tertiary structure remarkably similar to that observed for the first two helices of B-domain in the B-domain/Fc complex [Deisenhofer, J. (1981) Biochemistry 20, 2361-2370], although it is significantly less stable. Based on this structure, we have improved on Z38 by designing a 34-residue disulfide-bonded variant (Z34C) that has dramatically enhanced stability and binds IgG with 9-fold higher affinity. The improved stability of Z34C led to NMR spectra with much greater chemical shift dispersion, resulting in a more precisely determined structure. Z34C, like Z38, has a structure virtually identical to the equivalent region from native protein A domains. The well-defined hydrophobic core of Z34C reveals key structural features that have evolved in this small, functional domain. Thus, the stabilized two-helix peptide, about half the size and having one-third of the remaining residues altered, accurately mimics both the structure and function of the native domain.

Selected figure(s)

Figure 2.
Fig. 2. Overlay of the fingerprint region of COSY spectra for Z38 (black) and Z34C (red). Spectra were acquired under identical conditions at 8°C (pH 5.1). Selected crosspeaks are labeled for Z34C; arrows show the location of the same crosspeak in Z38. Complete 1H resonance assignments are available from the authors upon request.

Figure 4.
Fig. 4. NMR structure ensembles for (A) Z38 and (B) Z34C. In each case, 24 models are shown aligned using the backbone atoms of residues 10-36. Shown also are the coordinates for residues 7-38 from the^ crystal structure of the B-domain/Fc complex (red) (6). The^ disordered N-terminal residues 1-5 from Z38 are colored gray. Side chains from the hydrophobic core of Z34C are shown (Phe-6, Cys-10, Phe-14, Ala-17, Leu-18, Leu-23, Ile-32, Ile-35, and Cys-39). (C) The minimized mean structure of Z34C showing all side chains colored by amino acid type: hydrophobic (yellow), positively charged^ (blue), negatively charged (red), and polar (green); only those^ that are labeled are well defined in the NMR ensemble with 1^angular order parameters >0.9. Note that only the 1 = 60° orientation for Phe-14 is shown, but this side chain also exists in the 1^ = 180° conformation in solution. (D) Same as C, but rotated 90° with the Fc binding surface on top.

Figures were selected by an automated process.