Supplementary Discussion-1
RNA structure comparison of HutP and TRAP proteins
HutP recognizes two units of single stranded RNA, forming a novel triangular shape, on
both the top and bottom surfaces of the protein, whereas TRAP recognizes one unit of
single stranded RNA, forming a belt around the protein molecule. The HutP requires
UAG motifs separated by a four spacer nucleotides, whereas the TRAP requires
UAG/GAG motifs separated by a two or three spacer nucleotides. The HutP RNA has
an extended structure passing across the β-sheet along the HutP monomer, whereas the
RNA is recognized in the dimer interface in the case of TRAP. Essentially, the A and G
in the UAG motif are quite critical for the protein recognition in both HutP and TRAP.
The RNA segment (A4-G5) recognized by HutP superimposes well on the A2-G3 of the
RNA segment bound to TRAP, although their base orientations are slightly different
from each other (Supplementary Fig. S3).