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. Author manuscript; available in PMC: 2015 Oct 26.
Published in final edited form as: Nat Commun. 2015 Jul 9;6:7480. doi: 10.1038/ncomms8480

Figure 8. VapC-mt4-tRNA docking simulations.

Figure 8

(a) Predicted binding of a (VapC-mt4)2 (blue and green) to tRNAAla2 (Type I tRNA homologue, tRNAPhe model shown in orange; PDB accession code 4TNA) using a protein–RNA docking simulation programme 3dRPC. The consensus sequence 5′-ACUGC-3′ is highlighted in red and boxed. The upper right boxed magnification shows a 90°rotated view highlighting the proximity of the tRNA consensus sequence to the VapC monomer not thought to be involved in activity (green). The lower right boxed magnification is a detailed view of the cleavage site. The VapC-mt4 key residues, tRNA consensus sequence and the target nucleotides are shown as sticks, with a black triangle indicating the cleavage site. (b) Predicted binding of a (VapC-mt4)2 (blue and green) to tRNASer24/Ser26 (Type II tRNA homologue, tRNALeu model shown in orange; PDB accession code 3UZ3). The expanded variable loop of tRNASer26 is depicted in orange outline and the consensus sequence 5′-ACUGC-3′ is highlighted in red. The boxed magnification is a detailed view of the cleavage site showing the VapC-mt4 key residues, the tRNALeu consensus sequence and the target nucleotides are shown in sticks, with a black triangle indicating the cleavage site. The extrapolated position of a divalent cation is shown as a purple sphere in both a,b. (c) A comparison of (VapC-mt4)2 binding, highlighting the positional shift in tRNA binding depending on the target tRNA type (grey, tRNAAla2; red, tRNASer24/Ser26). The presence of expanded variable loop in tRNASer26 (shown in red outline) influences the binding of VapC-mt4 (positions lower in anticodon loop) possibly explaining the difference observed in target cleavage sites. Convention when numbering tRNA bases dictates that the anticodon bases are numbered 34–36. This convention is followed in a–c. Note however that in the case of tRNASer26/Ser24 (b,c) the actual base numbers for the anticodon are 35–37.