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

Myllykoski, Matti; Kursula, Petri

Some viral and eukaryotic 2H enzymes cleave the 2 0 -5 0 -phosphodiester bond of 2 0 -5 0 -polyadenylates [11] [12] [13] . Structural data [29] from these enzymes incidate that the 2 0 ,5 0 -adenosine bisphophate substrate binds along the opposite side of the active site, compared to LigT and CNPase (Fig 7A) . In CNPase, the side used for 2 0 ,5 0 -adenosine bisphophate in these enzymes is blocked by the α7 helix, which coordinates the nucleophilic water. In LigT, this opposite side is open, and there would be room for a larger nucleophile than water, even though recent data suggest that short RNA molecules would not act as nucleophiles in LigT [22] . The central phosphate moiety sits nearly identically on top of the HxTx motifs, however. Combining both binding modes by superposition, interesting conservation can be observed (Fig 7A) . For example, LigT Trp82 is in a perfect position to stack against a base, and Arg120 is conserved. In the NADP + complex, we actually observe unidentified electron density of a stacking interaction, modeled as a fragment of NADP + , on top of Trp82, which could reflect low-affinity binding of some moiety in NADP + . These observations highlight several possible sites for interaction between phosphate, sugar, and base moieties in RNA with residues lining the active-site groove in LigT.