2DD2

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack

Summary for 2DD2

• Entry DOI: 10.2210/pdb2dd2/pdb
• Related: 1XV0 2DD1 2DD3
• NMR Information: BMRB: 6979
• Descriptor: 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3', 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P))-3' (2 entities in total)
• Functional Keywords: alternating, conformation exchange, dynamics, sheared aa pair, sheared ga pair, thermodynamics, rna secondary structure, a-minor motif, kink-turn, rna
• Total number of polymer chains: 2
• Total formula weight: 6440.99

Authors

Chen, G.,Kennedy, S.D.,Krugh, T.R.,Turner, D.H. (deposition date: 2006-01-19, release date: 2006-06-13, Last modification date: 2024-05-29)

Primary citation

Chen, G.,Kennedy, S.D.,Qiao, J.,Krugh, T.R.,Turner, D.H.
An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA
Biochemistry, 45:6889-6903, 2006

PubMed Abstract: A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.

PubMed: 16734425
DOI: 10.1021/bi0524464

Experimental method

SOLUTION NMR