Structure of Alzheimer's disease amyloid precursor protein copper-binding domain at atomic resolution

Abstract

Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer's disease, as its cleavage generates the Abeta peptide that is toxic to cells. APP is able to bind Cu2+ and reduce it to Cu+ through its copper-binding domain (CuBD). The interaction between Cu2+ and APP leads to a decrease in Abeta production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 A) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu2+ reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Abeta production.

Figure 1

A ribbon diagram of CuBD in stereoview. The N- and C-termini are labelled. The α-helix is coloured blue (residues 147–160) and the β-strands are depicted by pink arrows (β1, residues 133–139; β2, 163–174; β3, 177–188). The copper-binding residues His147, His151 and Tyr168 are coloured light blue, blue and gold, respectively. The three disulfides are shown as sticks (from left to right: Cys133–Cys187, Cys158–Cys186 and Cys144–Cys174). The diagram was prepared using PyMOL (DeLano Scientific LLC, USA).

Figure 2

An illustration of the atomic motions in CuBD. Atomic motions are depicted by means of 50% probability vibration ellipsoids. The ellipsoids are coloured according to isotropic B factors, from blue (B factor of 5 Ų) through green to yellow (B factor exceeding 25 Ų). The figure was prepared with the online program PARVATI (Merritt, 1999 ▶).

Figure 3

The copper-binding site at atomic resolution (a) and a comparison with the previous 1.6 Å resolution structure (b) and the Cu²⁺-bound CuBD structure (c). All the figures are presented in stereoview and were prepared using PyMOL (DeLano Scientific LLC, USA). The atomic resolution structure is coloured in the standard atomic colouring scheme. In (a), the blue mesh represents 2F _obs − F _calc density contoured at 1.5σ. In (b), the 1.6 Å resolution structure is coloured in aqua throughout. In (c), the C atoms of the Cu²⁺-bound CuBD structure are coloured purple, the Cu²⁺ ion orange and the water ligands grey.