A pseudoknot-compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center

The RNA secondary structure is not confined to a system of the hairpins and can contain pseudoknots as melt as topologically equivalent slipped-loop s tructure (SLS) conformations. ii specific primary structure that directs fo lding to the pseudoknot or SLS is called SL-palindrome (SLP). Using a compu ter program for searching the SLP in the genomic sequences, 419 primary str uctures of large ribosomal RNAs from different kingdoms (prokaryota, eukary ota, archaebacteria) as well as plastids and mitochondria were analyzed. A universal site was found in the peptidyltransferase center (PTC) capable of folding to a pseudoknot of 48 nucleotides in length. Phylogenetic conserva tion of its helices (concurrent replacements with no violation of base pair ing, covariation) has been demonstrated. We suggest the reversible folding- unfolding of the pseudoknot for certain stages of the ribosome functioning. (C) 1999 Federation of European Biochemical Societies.