Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family

Abstract

We present here the structure of Yer010c protein of unknown function, solved by Multiple Anomalous Diffraction and revealing a common fold and oligomerization state with proteins of the regulator of ribonuclease activity A (RraA) family. In Escherichia coli, RraA has been shown to regulate the activity of ribonuclease E by direct interaction. The absence of ribonuclease E in yeast suggests a different function for this family member in this organism. Yer010cp has a few supplementary secondary structure elements and a deep pseudo-knot at the heart of the protein core. A tunnel at the interface between two monomers, lined with conserved charged residues, has unassigned residual electron density and may constitute an active site for a yet unknown activity.

Figure 1.

(A) Ribbon stereo representation of the structure of the Yer010cp monomer. The N- and C-terminal helices are colored in orange and in red, respectively. The second α-helical layer is colored purple. The (S1), (S2), and (S3) sheets are colored green, light blue, and dark blue, respectively. Protein figures are generated by Pymol (http://www.pymol.org). (B) Structural superposition of Yer010cp homologs in the same orientation as A: E. coli (dark blue), T. thermophilus (green), M. tuberculosis (light blue), and V. cholerae (purple). (C) Ribbon representation of the Yer010cp trimer. The three chains are in different colors. (D) Surface representation of the Yer010cp trimer. The surface is colored in increasing shades of red according to residue conservation (red most conserved) as determined by the consurf server (Glaser et al. 2003). (E) Close-up view of the conserved pocket between two monomers in surface (right) or cartoon (left) representation. The residual electron density (F_o−F_c map contoured at 3 σ) is shown in green. The residues lining the tunnel are shown in stick representation.

Figure 2.

Alignment of the Yer010cp sequence to eukaryotic (Candida albicans, Neurospora crassa, A. thaliana) to the E. coli and T. thermophilus orthologs whose structure has been solved and to the RraA-like domains in L. pneumophila and M. barkeri, which are fused to another protein domain (excluded from the alignment).