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A pseudoknot‐compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center
Author(s) -
Ivanov V.I,
Bondarenko S.A,
Zdobnov E.M,
Beniaminov A.D,
Minyat E.E,
Ulyanov N.B
Publication year - 1999
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(99)00166-0
Subject(s) - pseudoknot , ribosome , folding (dsp implementation) , ribosomal rna , base pair , rna , protein secondary structure , nucleic acid secondary structure , nucleotide , biology , nucleic acid structure , chemistry , computational biology , crystallography , genetics , dna , biochemistry , gene , electrical engineering , engineering
The RNA secondary structure is not confined to a system of the hairpins and can contain pseudoknots as well as topologically equivalent slipped‐loop structure (SLS) conformations. A specific primary structure that directs folding to the pseudoknot or SLS is called SL‐palindrome (SLP). Using a computer program for searching the SLP in the genomic sequences, 419 primary structures of large ribosomal RNAs from different kingdoms (prokaryota, eukaryota, 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 conservation of its helices (concurrent replacements with no violation of base pairing, covariation) has been demonstrated. We suggest the reversible folding‐unfolding of the pseudoknot for certain stages of the ribosome functioning.