FrpD is an Iron-regulated outer membrane lipoprotein, which is highly conserved in a set of strains representative of all serogroups of Neisseria meningitidis. The biological function of FrpD remains unknown but FrpD is likely to participate in the anchoring of the Type I-secreted FrpC protein to the bacterial cell surface. FrpC belongs to the Repeat in Toxins (RTX) protein family and binds FrpD with very high affinity (Kd = 0.2 nM) . However, the mechanism of FrpD-FrpC interaction is unknown due to the absence of any structural information on these proteins. This project is aimed to determine the structure of the FrpD protein.
The native and Se-Met substituted variants of recombinant, truncated version FrpD43-271 protein were prepared and crystallized using the sitting-drop vapour-diffusion method. The crystals of native FrpD43-271 protein belong to the hexagonal space group P64, while the crystals of Se-Met substituted FrpD43-271 protein belong to the primitive orthorhombic space group P212121 . The crystal structures of native and SeMet labelled FrpD proteins were solved to an atomic resolution of 2.3 Å and 1.40 Å, respectively. The refined crystallographic models comprise 224 of the 229 residues with the one N-terminal and four C-terminal residues being disordered. The two refined structures are largely identical, with the coordinate root-mean-square deviation (r.m.s.d.) of 0.56 Å of over 224 aligned residues. FrpD protein displays a compact slightly concave globular shaped structure. The FrpD fold is based on three central β-sheets, flanked by 3 short helices and one long C-terminal α-helix. Structure-based analysis was made using A DALI (distance matrix alignment server) and PDBeFold server database search for similar three-dimensional structures using the refined model of FrpD as the target. Performed analysis indicated that FrpD fold did not contain the topology sufficiently similar to establish structural homology with other known proteins, indicating that FrpD corresponds to a novel fold.
This work was supported by the Grant Agency of the Czech Republic P207/11/0717, Ministry of Education of the Czech Republic (LC06010 and MSM6007665808) and by the Academy of Sciences of the Czech Republic (AV0Z60870520, AV0Z50520514 and AV0Z40550506).