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Alzheimer's amyloid precursor protein copper-binding domain

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spinqualitylabelsall models PDB ID 2fkl Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
2fkl, resolution 2.50Å ()
Gene:	APP (Homo sapiens)
Related:	1owt, 2fjz, 2fk1, 2fk2, 2fk3
Structural annotation: Resources: InterPro : Ipr008154, Ipr013803, Ipr015849, Ipr011178, Ipr002223, Ipr008155 Pfam : PF02177 UniProt : P05067
Functional annotation: Cellular component: coated pit extracellular region integral to plasma membrane integral to membrane membrane cell surface Biological process: cell adhesion neuromuscular process apoptosis cellular copper ion homeostasis endocytosis Notch signaling pathway Molecular function: endopeptidase inhibitor activity identical protein binding binding protein binding serine-type endopeptidase inhibitor activity zinc ion binding heparin binding metal ion binding iron ion binding copper ion binding
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

PyMol representation of 2fkl

IntroductionIntroduction

2FKL is located in a transmembrane protein called APP for Amyloid precursor protein. This domain going from residue 124 to 189 is localized in the extracellular part of APP just between the Growth Factor Domain (GFD) and the Acidic domain, in a region called Cu-Binding Domain which is able to bind Cu and Zinc.

This proteins plays a major role into the development of Alzheimer disease. APP cleavage by BACE and gamma secretase gives ended rise to the Aβ peptide, which forms at the end an aggregation of amyloid plaques .

As the interaction between copper ion and APP can modulate the production of Aβ peptide and also the progression of Alzheimer disease, structural studies of the Cu-binding Domain of this protein give a lot of information for the development of novel therapeutics.

StructureStructure

spinqualitylabelsall models 2fkl Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Secondary structureSecondary structure

2fkl is constituted by two chains called A and B . Both chains have the same organization. Each chain also contains an going from residue 147 to 159 packed against a triple-strand beta sheet. The strand going from residue 133 to 139, the going from residue 162 to 167, and the going from residue 181 to 188. There is one more Beta sheet, , formed by the residues 127 to 139 of the B chain.

Tertiary structureTertiary structure

The three dimensional structure of the Cu-Binding Domain was first determined by resonance multidimensional NMR spectroscopy . More recently, the determination of the crystallographic structure permits to define the molecular interaction between the Cu-Binding Domain and copper. Between the Cysteine 133 and the Cystein 187 we can find a which links and between cystein 158 and cystein186 which links the alpha helix to the strand Beta 3. Between the cysteine 144 and the cysteine 174 we can describe another .

In order to improve the stabilization of this structure there is a small which contains different residues from each seconday structure. (Leu 136, Trp 150, Val 153, Ala154, Leu 165, Met 170, Val 182 and Val 185)

The study of the structure also showed on the surface of the Cu-Binding Site different regions (Glu 156, Glu 160, Glu 183 , Asp 167 et Asp 131 ) and charged(Lys 132, Lys134, Lys161, His 147, His 151 and Lys 155)

His147, His151, Tyr168, Met170 are residues that have been identified as able to bind copper. Those four residues are forming a also called tetrahedral coordination sphere.

Quaternary structureQuaternary structure

Finally, quaternary structure is formed by two chain A and B, however, there are a few contacts between those two chains. The strand B0 allows thanks to hydrogen bounds some of those interactions. There are also some Van der Waals interaction betweens diffenents aminoacids located on the two chains such as :
His147 (A) and Phe135 (B)
Gly175 (A) and Leu171 (B)
Asp177 (A) and His137 (B)

Biological roleBiological role

2FKL belongs to the domain of APP which is able to bind Cu and zinc. Copper is an important metal to health. It acts as an indispensable catalytic and structural cofactor that drives many biological functions of our organism. But in particular situations like overcconcentration it can also become toxic for the cell.

Fig.1: Cu(I) binding geometry

Thanks to its extracellular Cu-Binding Domain (CuBD) constituated by the amino acids describe above, APP can modulate copper transport and storage. The Cu-binding domain of the apo protein (represented in grey in the fig.1 ) seems to be able to fixe Cu(II) and to reduce it into Cu(I). More precisely, the Tyr 168, the His 147 and the His 151 participate in Cu(II) binding but not the Methionine 170. In addition, two molecules of water, one axial and one equatorial (noted Ax and Eq on Fig.1) play an important role in (represented also in standard atomic colouring in Fig 1)(PDB ID : 2fk1). It results that the arrangement of the atoms involved in the Cu(II) binding adopts a square pyramidal geometry which can be classified as a Type 2 non-blueCu(II) center. In this type of center Cu(II) is bound by two or three nitrogene ligands and one or two oxygen ligands. Met170 is supposed to act as an electron donor to Cu(II).

Fig.2: Cu(I) binding geometry

In the (represented in grey in Fig.2)(PDB id 2fk2), there is no axial water molecules ; the site adopts also a distorted square planar arrangement which is unfavorable for Cu(I) suggesting that this state is not favorable and can lead to the tranfert of the Cu (I) to others proteins.In Fig.2 standard atomic colouring reprensents the Cu(II)binding form.

Medical ImplicationMedical Implication

fig 3 : Schematic representation of APP processing

An Alzheimer disease is responsible for the most comon form of dementia among old people. Causes of this disease are not clear but genes and environmental factors seem to play a major role. It is characterized by extensive neuronal death, shrinkage of the brain and also the presence of amyloid plaques into the brain These plaques are concentrated with Aβ peptide which results from the anormal cleavage of APP by successive action of the β and γ secretases, illustrated on fig 3.The alteration in copper homostasis is directly related to the progression of Alzheimer disease. The impact of Cu(II) on the aggregation of Aβ peptide is still discussed even if Cu(II) is find in elevated concentration in these plaques. For more information you can follow the link : Alzheimer disease

The differents domains involved into the Aβ dimerisation aren't yet wery well known, but it seems that E1 and E2 are playing a major role. E1 contains the copper-binding site domain and also the Growth Factor-like Domain, rather than E2 contains the Central APP domain. Those two regions are located in the extracellurlar space.

If the CuBD (located in E1 region) does contribute to APP dimerisation without Cu ions, that means that the Cu binding may reduce Aβ production, either by shifting the monomer-dimer equilibrium to favor monomer form, or by re-orienting the dimer form, which disfavours the Aβ production.

Additionnal ResourcesAdditionnal Resources

PDB file of 2fkl
PDB file of 2fk1
PDB file of 2fk2
Alzheimer disease

ContributorsContributors

Milène Walter, Andréa Mc Cann