Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs

On the occurrence of the T-loop RNA folding motif in large RNA molecules

“…between the two sets of coordinates. As expected, besides the motifs identified by Nagaswamy and Fox (2002), we found additional occurrences (Table 1). For some occurrences, including some reported by Nagaswamy and Fox (2002), it was difficult to ascertain from the structure whether these examples really contained the required base pair, and hence they were excluded from the comparison.…”

“…As expected, besides the motifs identified by Nagaswamy and Fox (2002), we found additional occurrences (Table 1). For some occurrences, including some reported by Nagaswamy and Fox (2002), it was difficult to ascertain from the structure whether these examples really contained the required base pair, and hence they were excluded from the comparison. In the case of the 335-339 loop in 23S rRNA, which conforms to the sequence consensus, it was hard to conclude that it forms a similar structure to the one in the T-loop motif in tRNA; therefore, it was excluded from our analysis (Fig.…”

“…of 1.3Å). Table 1 also shows that the non-Watson-Crick base pair that flanks the U-turn is not necessarily a trans W.-C./Hoogsteen UA, as proposed by Nagaswamy and Fox (2002). For example, a trans W.-C./ Hoogsteen CA base pair is found in the flanking position of the 505-509 T-loop of the 23S rRNA (1JJ2), and trans W.-C./Hoogsteen AA base pairs are observed in the 187-191 T-loop motif of the S-domain of the RNase P (PDB 1NBS) and in the TC-loop of the yeast initiator tRNA (PDB 1YFG).…”

“…Rapid progress in the determination of structures of large RNA molecules has allowed characterization of new structural motifs, including the tetraloop-tetraloop receptor (Pley et al 1994;Cate et al 1996a), ribose zippers (Cate et al 1996a), dinucleotide platforms (Cate et al 1996b), A-minor motifs (Doherty et al 2001;Nissen et al 2001), kink-turns (Klein et al 2001), and others (Hermann and Patel 1999;Moore 1999). The T-loop RNA folding motif was recently identified in a number of RNA structures (Nagaswamy and Fox 2002). It contains a U-turn (both UNR and GNR U-turns are allowed) flanked by a noncanonical base pair and has a distinctive threedimensional structure (Fig.…”

“…In the original work of Nagaswamy and Fox (2002) describing the occurrence of the T-loop motif, the search for the T-loop motif was confined to sequences in which the base pair flanking the U-turn (Fig. 1, bases 1 and 5) forms a UA base pair, thus excluding any other base pair that might occur at this position.…”