Figure 1. Evolutionary and structural divergence among the C.elegans PUF protein family.

(A) Dendrogram of C. elegans PUF proteins based on alignment of primary sequences. The four clades are indicated: FBF, containing FBF-2 (blue and maroon); PUF-8/9, containing PUF-8 (blue and yellow); PUF-3/11 (cyan) and PUF-5/6/7 (mauve). (B) FBF-2 forms a flatter RNA-binding surface to bind to a 9-nt FBE sequence and accommodates an extra nucleotide opposite PUM repeats R4 and R5. Schematic illustration (left) and ribbon diagram (middle) of FBF-2 in complex with FBE RNA (PDB ID 3V74). Repeats are colored alternately red and blue. RNA recognition side chains from each PUM repeat are shown. The RNA is shown as a stick representation colored by atom type (maroon, carbon; red, oxygen; blue, nitrogen; orange, phosphorus). Carbon atoms for nucleotides 5 and 6 are green. Structural superposition of repeats R5-R8 of PUF-8 and FBF-2 demonstrates the flatter curvature of the RNA-binding surface of FBF-2. The RNA-binding helices of PUF-8 (gold) and FBF-2 (red) are shown as cylinders (right). (C) Crystal structure of PUF-8 in complex with 8-nt PBE RNA reveals modular 1:1 recognition of RNA by PUM repeats and a curvature similar to PUM1. Schematic illustration (left) and ribbon diagram (middle) of PUF-8 in complex with PBE RNA. Repeats are colored alternately gold and blue. RNA recognition side chains from each PUM repeat are shown. The RNA is colored as in panel B, except carbon atoms are gold, The RNA base at the 5^th position, which stacks with the 4^th base and turns away from the protein surface, is shown with green carbon atoms. Superposition of the crystal structures of PUF-8 and human PUM1 demonstrates similar curvature. The RNA-binding helices of PUF-8 (gold) and PUM1 (blue) are shown as cylinders (right).