Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family

Background: L1 is an important primary rRNA-binding protein, as well as a t ranslational repressor that binds mRNA. It was shown that L1 proteins from some bacteria and archaea are functionally interchangeable within the ribos ome and in the repression of translation. The crystal structure of bacteria l L1 from Thermus thermophilus (TthL1) has previously been determined. Results: We report here the first structure of a ribosomal protein from arc haea, L1 from Methanococcus jannaschii (MjaL1). The overall shape of the tw o-domain molecule differs dramatically from that of its bacterial counterpa rt (TthL1) because of the different relative orientations of the domains. T wo strictly conserved regions of the amino acid sequence, each belonging to one of the domains and positioned close to each other in the interdomain c avity of TthL1, are separated by about 25 Angstrom in MjaL1 owing to a sign ificant opening of the structure, These regions are structurally highly con served and are proposed to be the specific RNA-binding sites. Conclusions: The unusually high RNA-binding affinity of MjaL1 might be expl ained by the exposure of its highly conserved regions. The open conformatio n of MjaL1 is strongly stabilized by nonconserved interdomain interactions and suggests that the closed conformations of L1 (as in TthL1) open upon RN A binding. Comparison of the two L1 protein structures reveals a high confo rmational variability of this ribosomal protein. Determination of the MjaL1 structure offers an additional variant for fitting the L1 protein into ele ctron-density maps of the 50S ribosomal subunit.