Figure 2.

Comparison of the TMEV 2A structure with the EMCV orthologue reveals a divergent RNA-binding surface and C-terminal region. (A) Amino acid sequence alignment of selected divergent TMEV-like (upper) and EMCV-like (lower) cardiovirus 2A protein sequences, guided by the structural alignment of EMCV and TMEV 2A proteins. Known secondary structures are indicated above the corresponding sequence for EMCV and TMEV proteins. N- and C-terminal residues not observed in the structures are greyed out. Conservation is highlighted in blue. Local motifs of functional significance are highlighted and annotated. (B) Comparison of RNA-binding residues in EMCV 2A (28) (beige) with equivalent surface in TMEV 2A (pale blue). Residues involved in RNA binding come from three regions of the EMCV protein as indicated in (A) (shown as red, crimson and brown sticks). TMEV residues that may be functionally-equivalent are shown as sticks (cyan). (C) Surface of TMEV 2A, coloured by conservation from highly conserved (purple) to variable (teal) amongst the divergent TMEV-like sequences listed in A. Highly conserved, surface-accessible residues are labelled and shown as sticks. (D) Comparison of the YxxxxLΦ binding motif in 4E-BP1 and putative motif in TMEV 2A. The crystal structure of the complex between eIF4E and 4E-BP1 is shown (green and blue, respectively) with 2A (pale blue) docked via least-squares superposition of the YxxxxLΦ motif. A local surface cutaway, removing a section of β3 (dashed lines), shows the buried location of Y119. Inset:Contrast between the two different helical conformations of the putative 2A YxxxxLΦ motif and the 4E-BP1 YxxxxLΦ motif, in a compact α-helical conformation. (E) Conformational differences between the C-terminal putative YxxxxLΦ motif in TMEV 2A (pale blue) and EMCV 2A (wheat).