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. 2019 Jul 11;47(16):8770–8784. doi: 10.1093/nar/gkz583

Figure 1.

Figure 1.

Two molecules of Puf1 recognize a dual UAAU motif. (A) Schematic drawing of the structural domains of Puf1 protein and the sequence of a dual UAAU motif RNA. Puf1 contains an N-terminal RRM (blue) and C-terminal PUM-HD (purple and gray ovals) beginning with an α-helical region (αN, green). Disordered regions are predicted between the RRM and the αN domain and after the PUM-HD. Puf1 protein constructs used in our studies are indicated. The two UAAU motifs in the RNA sequence are colored as in (B), and the nucleotide numbering used in the text is shown. (B) Crystal structure of the Puf1 PUM-HD in complex with a dual UAAU motif. Each of the two Puf1 PUM-HD proteins recognizes one of the UAAU sequences. We designate molecule A as the Puf1 PUM-HD interacting with the 5′-UAAU and molecule B as that interacting with the downstream UAAU-3′. The proteins are shown as ribbon diagrams with the N-terminal α-helical repeats (R1′ and R2-R5) colored alternately purple and light blue and non-RNA-binding repeats (R6-R8) colored gray. The N- and C-termini of the Puf1 PUM-HD are indicated by blue and red spheres, respectively. The αN region is colored green, and a helix encoded by the vector sequence is shown in beige. The RNA is shown as a cartoon highlighting the two UAAU motifs. (C) Conserved surfaces of the Puf1 PUM-HD interact with dual UAAU motif RNA. The two Puf1 molecules are shown as surface representations colored by degree of sequence conservation calculated using the ConSurf server (55). Highly conserved residues are colored maroon and weakly conserved residues are colored cyan.