Fig. 2: The interaction of the tRNA anticodon-stem loop with ADAT2/3. | Nature Communications

Fig. 2: The interaction of the tRNA anticodon-stem loop with ADAT2/3.

From: Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3

Fig. 2

a The anticodon loop (ACL) bound to TbADAT2/3 (black) is distorted with respect to free tRNA (brown; PDB: 1EHZ) but resembles the ACL bound to bacterial TadA (gray; PDB: 2B3J), all cartoon-stick representation. b A deep cleft in the dimer interface accommodates the ACL. Colors as in Fig. 1, ADAT2/3 model as surface representation, tRNA as cartoon with anticodon loop bases shown. c The deformed ACL bound to the TbADAT2/3, backbone in cartoon and bases in stick representation. d Schematic overview of the anticodon stem loop (ACSL) and its interactions with TbADAT2/3. Zinc coordinating site highlighted in yellow. e–g Comparison of the active-site pockets of Tb and MmADAT2/3 and TadA in the same orientation: e TbADAT2/3 with tRNA cytosine-base shown; f apo-MmADAT2/3 (PDB: 7NZ7), with the conserved H298MmADAT3 as the only ADAT3 residue present in the active site; g bacterial SaTadA (PDB: 2B3J) with nebularine bound, with M92SaTadA훃 residue contributed by the second protomer of the homodimer. Residue side chains colored by heteroatom with zinc atoms in yellow.

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