8ITS

Crystal structure of DUF-3268 k-junction

Summary for 8ITS

• Entry DOI: 10.2210/pdb8its/pdb
• Descriptor: RNA (46-MER), MAGNESIUM ION (3 entities in total)
• Functional Keywords: k-junction, k-turn, rna motif, rna
• Biological source: bacterium
• Total number of polymer chains: 1
• Total formula weight: 15009.90

Authors

Li, M.,Lilley, D.M.J.,Huang, L. (deposition date: 2023-03-22, release date: 2024-03-27, Last modification date: 2025-04-09)

Primary citation

Li, M.,Deng, J.,Peng, X.,Wang, J.,Wilson, T.J.,Huang, L.,Lilley, D.M.J.
Structure and ion-dependent folding of k-junctions.
Rna, 29:1411-1422, 2023

PubMed Abstract: k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of and thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the and riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly.

PubMed: 37311599
DOI: 10.1261/rna.079678.123

Experimental method

X-RAY DIFFRACTION (1.94 Å)