4AOB

SAM-I riboswitch containing the T. solenopsae Kt-23 in complex with S- adenosyl methionine

Summary for 4AOB

• Entry DOI: 10.2210/pdb4aob/pdb
• Descriptor: SAM-I RIBOSWITCH, BARIUM ION, POTASSIUM ION, ... (6 entities in total)
• Functional Keywords: translation, k-turn, rna
• Biological source: THERMOANAEROBACTER TENGCONGENSIS
• Total number of polymer chains: 1
• Total formula weight: 33345.37

Authors

Schroeder, K.T.,Daldrop, P.,McPhee, S.A.,Lilley, D.M.J. (deposition date: 2012-03-25, release date: 2012-05-09, Last modification date: 2023-12-20)

Primary citation

Schroeder, K.T.,Daldrop, P.,Mcphee, S.A.,Lilley, D.M.J.
Structure and Folding of a Rare, Natural Kink Turn in RNA with an Aa Pair at the 2B2N Position.
RNA, 18:1257-, 2012

PubMed Abstract: The kink turn (k-turn) is a frequently occurring motif, comprising a bulge followed by G•A and A•G pairs that introduces a sharp axial bend in duplex RNA. Natural k-turn sequences exhibit significant departures from the consensus, including the A•G pairs that form critical interactions stabilizing the core of the structure. Kt-23 found in the small ribosomal subunit differs from the consensus in many organisms, particularly in the second A•G pair distal to the bulge (2b•2n). Analysis of many Kt-23 sequences shows that the frequency of occurrence at the 2n position (i.e., on the nonbulged strand, normally G in standard k-turns) is U>C>G>A. Less than 1% of sequences have A at the 2n position, but one such example occurs in Thelohania solenopsae Kt-23. This sequence folds only weakly in the presence of Mg²⁺ ions but is induced to fold normally by the binding of L7Ae protein. Introduction of this sequence into the SAM-I riboswitch resulted in normal binding of SAM ligand, indicating that tertiary RNA contacts have resulted in k-turn folding. X-ray crystallography shows that the T. solenopsae Kt-23 adopts a standard k-turn geometry, making the key, conserved hydrogen bonds in the core and orienting the 1n (of the bulge-proximal A•G pair) and 2b adenine nucleobases in position facing the opposing minor groove. The 2b and 2n adenine nucleobases are not directly hydrogen bonded, but each makes hydrogen bonds to their opposing strands.

PubMed: 22539525
DOI: 10.1261/RNA.032409.112

Experimental method

X-RAY DIFFRACTION (2.95 Å)