Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase

Myllykoski, Matti; Kursula, Petri

Earlier, we identified a possible RNA-binding groove in mouse CNPase, which additionally has a polynucleotide kinase-like domain [17] . The surface analysis of LigT, specifically looking at electrostatics, aromatic surface residues, and basic residues, indicates that a similar surface extends away from the LigT active site. The active site is formed at the bottom of a groove lined with basic and aromatic residues, and this groove has a very high positive electrostatic potential (Fig 7B and 7C ). These characteristics fit well to the hypothesis of RNA binding. The substrate of LigT in an RNA ligation reaction is an RNA molecule, for which the 3 0 -terminal residue, with a 2 0 ,3 0 -cyclic phosphate group, sits in the active site. The orientation of the reaction products 2 0 -AMP and NADP + in the active site indicates the direction, into which an RNA molecule would continue, considering the last residue sits in the active site. Likely participants in RNA binding include several aromatic and Arg residues lining the active-site groove.