6XX2

Crystal structure of the c-Src SH3 domain H122R-Q128K mutant in complex with Cu(II) at pH 7.5 co-crystallized with methyl beta-cyclodextrin

Summary for 6XX2

• Entry DOI: 10.2210/pdb6xx2/pdb
• Related PRD ID: PRD_900086
• Descriptor: Proto-oncogene tyrosine-protein kinase Src, Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-3-O-methyl-alpha-D-glucopyranose, COPPER (II) ION, ... (4 entities in total)
• Functional Keywords: beta barrel, sh3 domain, protein binding
• Biological source: Gallus gallus (Chicken)
• Total number of polymer chains: 1
• Total formula weight: 8240.33

Authors

Camara-Artigas, A. (deposition date: 2020-01-26, release date: 2020-04-22, Last modification date: 2024-01-24)

Primary citation

Plaza-Garrido, M.,Salinas-Garcia, M.C.,Martinez, J.C.,Camara-Artigas, A.
The effect of an engineered ATCUN motif on the structure and biophysical properties of the SH3 domain of c-Src tyrosine kinase.
J.Biol.Inorg.Chem., 25:621-634, 2020

PubMed Abstract: Metal binding to sites engineered in proteins can provide an increase in their stability and facilitate new functions. Besides the sites introduced in purpose, sometimes they are present accidentally as a consequence of the expression system used to produce the protein. This happens with the copper- and nickel-binding (ATCUN) motif generated by the amino-terminal residues Gly-Ser-His. This ATCUN motif is fortuitously present in many proteins, but how it affects the structural and biophysical characterization of the proteins has not been studied. In this work, we have compared the structure and biophysical properties of a small modular domain, the SH3 domain of the c-Src tyrosine kinase, cloned with and without an ATCUN motif at the N terminus. At pH 7.0, the SH3 domain with the ATCUN motif binds nickel with a binding constant K = 28.0 ± 3.0 mM. The formation of the nickel complex increases the thermal and chemical stability of the SH3 domain. A comparison of the crystal structures of the SH3 domain with and without the ATCUN motif shows that the binding of nickel does not affect the overall structure of the SH3 domain. In all crystal structures analyzed, residues Gly-Ser-His in complex with Ni show a square planar geometry. The CD visible spectrum of the nickel complex shows that this geometry is also present in the solution. Therefore, our results not only show that the ATCUN motif might influence the biophysical properties of the protein, but also points to an advantageous stabilization of the protein with potential biotechnological applications.

PubMed: 32279137
DOI: 10.1007/s00775-020-01785-0

Experimental method

X-RAY DIFFRACTION (1.25 Å)