Crystal structure of RNA 3 '-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology

Background: RNA cyclases are a family of RNA-modifying enzymes that are con served in eucarya, bacteria and archaea. They catalyze the ATP-dependent co nversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase inter mediate. These enzymes might be responsible for production of the cyclic ph osphate RNA ends that are known to be required by many RNA ligases in both prokaryotes and eukaryotes. Results: The high-resolution structure of the Escherichia coli RNA S'-termi nal phosphate cyclase was determined using multiwavelength anomalous diffra ction. Two orthorhombic crystal forms of E. coli cyclase (space group P2(1) 2(1)2(1) and P2(1)2(1)2) were used to solve and refine the structure to 2.1 Angstrom resolution (R factor 20.4%; R-free 27.6%). Each molecule of RNA c yclase consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel cc helices and a four-stranded beta sheet; this fold was previously identified in translation initiation facto r 3 (IF3). The large domain is similar to one of the two domains of 5-enolp yruvylshikimate-3-phosphate synthase acid UDP-N-acetylglucosamine enolpyruv yl transferase. The smaller domain uses a similar secondary structure eleme nt with different topology, observed in many other proteins such as thiored oxin. Conclusions: The fold of RNA cyclase consists of known elements connected i n a new and unique manner. Although the active site of this enzyme could no t be unambiguously assigned, it can be mapped to a region surrounding His30 9, an adenylate acceptor, in which a number of amino acids are highly conse rved in the enzyme from different sources. The structure of E. coli cyclase will be useful for interpretation of structural and mechanistic features o f this and other related enzymes.