The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein.
BACKGROUND: The removal of introns from pre-mRNA is carried out by a large
macromolecular machine called the spliceosome. The peptidyl-prolyl cis/trans
isomerase PPIL1 is a component of the human spliceosome and binds to the
spliceosomal SKIP protein via a binding site distinct from its active site.
PRINCIPAL FINDINGS: Here, we have studied the PPIL1 protein and its interaction
with SKIP biochemically and by X-ray crystallography. A minimal linear binding
epitope derived from the SKIP protein could be determined using a peptide array.
A 36-residue region of SKIP centred on an eight-residue epitope suffices to bind
PPIL1 in pull-down experiments. The crystal structure of PPIL1 in complex with
the inhibitor cyclosporine A (CsA) was obtained at a resolution of 1.15 A and
exhibited two bound Cd(2+) ions that enabled SAD phasing. PPIL1 residues that
have previously been implicated in binding of SKIP are involved in the
coordination of Cd(2+) ions in the present crystal structure. Employing the
present crystal structure, the determined minimal binding epitope and previously
published NMR data, a molecular docking study was performed. In the docked model
of the PPIL1.SKIP interaction, a proline residue of SKIP is buried in a
hydrophobic pocket of PPIL1. This hydrophobic contact is encircled by several
hydrogen bonds between the SKIP peptide and PPIL1. CONCLUSION: We characterized
a short, linear epitope of SKIP that is sufficient to bind the PPIL1 protein.
Our data indicate that this SKIP peptide could function in recruiting PPIL1 into
the core of the spliceosome. We present a molecular model for the binding mode
of SKIP to PPIL1 which emphasizes the versatility of cyclophilin-type PPIases to
engage in additional interactions with other proteins apart from active site
contacts despite their limited surface area.