5FK4: Sam-i Riboswitch Bearing The H. Marismortui Kt-7 Variant 3bn Is Uu

Citation:
Abstract
k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G*A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures.
PDB ID: 5FK4Download
MMDB ID: 139521
PDB Deposition Date: 2015/10/14
Updated in MMDB: 2016/08
Experimental Method:
x-ray diffraction
Resolution: 2.43  Å
Source Organism:
Biological Unit for 5FK4: dimeric; determined by author and by software (PISA)
Molecular Components in 5FK4
Label Count Molecule
Nucleotide(1 molecule)
2
Sam-i Riboswitch
Molecule annotation
Chemicals (30 molecules)
1
2
2
28
* Click molecule labels to explore molecular sequence information.

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