The Archaeal sRNA Binding Protein L7Ae has a 3D Structure Very Similar to that of its Eukaryal Counterpart While Having a Broader RNA-binding Specificity

• Published in: Journal of molecular biology 2004-09, Vol.342 (3), p.757-773
• Main Authors: Charron, C., Manival, X., Cléry, A., Senty-Ségault, V., Charpentier, B., Marmier-Gourrier, N., Branlant, C., Aubry, A.
• Format: Article
• Language: English
• Subjects: 3D structure; Amino Acid Sequence; Archaea; Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Base Sequence; Binding Sites; Haloarcula marismortui - genetics; Haloarcula marismortui - metabolism; Humans; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; P. abyssi; Protein Conformation; protein L7Ae; Pyrococcus abyssi; Pyrococcus abyssi - genetics; Pyrococcus abyssi - metabolism; Ribonucleoproteins, Small Nuclear - chemistry; Ribonucleoproteins, Small Nuclear - genetics; Ribonucleoproteins, Small Nuclear - metabolism; Ribosomal Proteins - chemistry; Ribosomal Proteins - genetics; Ribosomal Proteins - metabolism; RNA, Archaeal - chemistry; RNA, Archaeal - genetics; RNA, Archaeal - metabolism; RNA, Ribosomal - chemistry; RNA, Ribosomal - genetics; RNA, Ribosomal - metabolism; RNA–protein interaction; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sequence Homology, Amino Acid; sRNA; Static Electricity
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2004.07.046

The ribosomal L7Ae protein of archaea has the peculiarity to be a component of the C/D and H/ACA snRNPs, that guide rRNA post-transcriptional modifications. Its yeast (Snu13p) and human (15.5 kDa protein) homologs are only found in C/D snoRNPs and the (U4/U6, U5) spliceosomal tri-snRNP. By using a large variety of RNAs, we compared the RNA-binding specificities of the recombinant Pyrococcus abyssi L7Ae and Saccharomyces cerevisiae Snu13 proteins. Unlike Snu13p, protein L7Ae binds terminal loops closed by two A:G and G:A pairs and canonical K-turn structures with similar efficiencies, provided that the terminal loop contains at least 5 nt. In contrast to Snu13p, binding of protein L7Ae to canonical K-turn structures is not dependent on the identity of the residue at position 2 in the bulge. The peculiar KT-15 motif of P. abyssi 23 S rRNA, that is recognized by L7Ae, does not associate with Snu13p. To get more information on the P. abyssi L7Ae protein, we solved its X-ray structure at 1.9 Å resolution. In spite of their sequence divergence, the free P. abyssi and bound H. marismortui proteins were found to have highly similar structures. Only a limited number of side-chain conformational changes occur at the protein–RNA interface upon RNA binding. In particular, one ion pair that is formed by residues Glu43 and Lys46 in the free protein is disrupted in the ribosomal 50 S subunit, so that, residue Glu43 can interact with the RNA residue G264. The Glu43-Lys46 ion pair of protein L7Ae belongs to a complex network of ion pairs that may participate to protein thermostability.