Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange

tRNA-guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of guanine-34 with the queuine precursor 7-aminomethyl-7-deazaguanine (preQ(1)), The crystal structure of TGT from Zymomonas mobilis was solved by multiple isomorphous replacement and refined to a crystallographic R-factor of 19% at 1.85 Angstrom resolution. The structure consists of an irregular (beta/alpha)(8)-barrel with a tightly attached C-terminal zinc-containing subdomain, The packing of the subdomain against the barrel is mediated by an alpha-helix, located close to the C-terminus, which displaces the eighth helix of the barrel. The structure of TGT in complex with preQ(1) suggests a binding mode for tRNA where the phosphate backbone interacts with the zinc subdomain and the U(33)G(34)U(35) sequence is recognized by the barrel. This model for tRNA binding is consistent with a base exchange mechanism involving a covalent tRNA-enzyme intermediate, This structure is the first example of a (beta/alpha)-barrel protein interacting specifically with a nucleic acid.