From the lab of  David M. J. Lilley

Latest News on k-turns

Click here for latest articles on kink turns in RNA on PubMed

2014

A critical base pair in k-turns that confers folding characteristics and correlates with biological function. Scott A. McPhee, Lin Huang & David M. J. Lilley Nature Communications. 5: 5127 (2014).

nk turns (k-turns) are widespread elements in RNA that mediate tertiary contacts by kinking the helical axis. We have found that the ability of k-turns to undergo ion-induced folding is conferred by a single base pair that follows the conserved A•G pairs, that is, the 3b•3n position. A Watson–Crick pair leads to an inability to fold in metal ions alone, while 3n = G or 3b = C (but not both) permits folding. Crystallographic study reveals two hydrated metal ions coordinated to O6 of G3n and G2n of Kt-7. Removal of either atom impairs Mg2+ - induced folding in solution. While SAM-I riboswitches have 3b•3n sequences that would predispose them to ion-induced folding, U4 snRNA are strongly biased to an inability to such folding. Thus riboswitch sequences allow folding to occur independently of protein binding, while U4 should remain unfolded until bound by protein. The empirical rules deduced for k-turn folding have strong predictive value.


2013

The functional exchangeability of pk- and k-turns in RNA structure. Daldrop P, Masquida B and Lilley DMJ . RNA Biol.. 10: 445-452 (2013).

Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme this is accomplished by a k-turn, while others have a different element called the pk-turn. RNase P of Thermotoga maritima has a pk turn. This is globally very similar to a k-turn in situ, but lacks all the standard A-minor hydrogen bonding and is not intrinsically kinked. It is shown that pk and k-turns can be functionally exchanged in RNase P and the SAM-I riboswitch.


The plasticity of a structural motif in RNA: Structural polymorphism of a kink turn as a function of its environment. Daldrop P, Lilley DMJ. RNA. 13: 357-364 (2013).

Shows that the great majority of k-turns fall into one of two classes, depending on whether N3 or N1 of adenine at the 2b position accepts the hydrogen bond donated by O2' of -1n. The crystal structure of Kt-7 engineered into the SAM-I riboswitch is presented, showing it to be an N3 structure, in contrast to its N1 structure in the ribosome.


Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. Baird, NJ, Ferré-D'Amaré, AR RNA 19: 167-176 (2013).

Interesting study of the folding of glycine riboswitches from Bacillus subtilis, Fusobacterium nucleatum, and Vibrio cholerae with and without the k-turn-containing linker between the two riboswitch domains. Concludes that the k-turn linker helps organize the quaternary structure of tandem riboswitches.

2012

An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches. Sherman EM, Esquiaqui J, Elsayed G, Ye JD. RNA 18: 496-507 (2012)

Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. Kladwang W, Chou FC, Das R. J Am Chem Soc. 134: 1404-1407 (2012).

Two papers showing that a sequence at the 5' end of the glycine riboswitch hybridizes to the linker region, creating a k-turn-containing duplex connecting the tandem repeats. See also the paper in 2013 from the Ferré D'Amaré lab. This brings the total of k-turn-containing riboswitches to four.


Structure and folding of a rare, natural kink turn in RNA with an A•A pair at the 2b•2n position. Schroeder KT, Daldrop P, McPhee SA, Lilley DMJ. RNA. 18: 1257-1266 (2012).

Determination of the crystal structure of a SAM-I riboswitch derivative containing Kt-23 of Thelohania solenopsae. This is a very rare natural example of a k-turn with an adenine at the 2n position, and the first structure of such a natural k-turn. It contains a non-hydrogen bonded A•A pair at the 2b•2n position. The crystal structure of the T. solenopsae k-turn has been added to the database.


Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein. Wang J, Fessl T, Schroeder KT, Ouellet J, Liu Y, Freeman AD, Lilley DMJ. Biophys J. 103: 2541-2548 (2012).

Attempting to answer the question of whether L7Ae acts on a k-turn by conformational selection or by induced fit. Single-molecule FRET fails to detect intermediates in folding down to a timescale of 8 ms, consistent with conformational selection.

September 2011

RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn. Schroeder KT, Daldrop P, Lilley DMJ. Structure. 19: 1233-1240 (2011).

Shows that tertiary interactions in the SAM-I riboswitch stabilize a k-turn in which G2n has been substituted by adenine. The crystal structure of the altered k-turn has been added to the database.

May 2011

Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches Smith KD, Shanahan CA, Moore EL, Simon AC, Strobel SA Proc. Natl. Acad. Sci. USA. 108: 7757-7762 (2011).

The structure of the k-turn has been added to the database.

February 2011

Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA. Wang J, Nikonowicz EP. J Molec Biol. 408 : 99-117 (2011).

The NMR structure of the k-turn has been added to the database.

November 2010

SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch Lu. C et al. J. Molec. Biol. 404: 803-818 (2010).

Ke and coworkers present a crystal structure of the B. subtilis SAM-I riboswitch showing the presence of the k-turn and a pseudoknot at a four-way junction. The k-turn structure has been added to the database.

August 2010

Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations. Spacková N, Réblová K, Sponer J. J Phys Chem B. 114:10581-93 (2010).

A computational investigation of a standard k-turn as a function of the binding of L7Ae and 15.5 kDa proteins.


Ribosomal protein L7Ae is a subunit of archaeal RNase P.Cho IM, Lai LB, Susanti D, Mukhopadhyay B, Gopalan V. Proc Natl Acad Sci USA. 107:14573-14578 (2010). The ribozyme RNase P of Methanococcus maripaludis has a k-turn that binds L7Ae. The authors show that addition of L7Ae increases the optimal reaction temperature and kcat/KM for cleavage of pre-tRNA by approximately 360-fold.

May 2010

Structure of the K-turn U4 RNA: a combined NMR and SANS study. Falb M, Amata I, Gabel F, Simon B, Carlomagno T. Nucleic Acids Res. 38: 6274-85 (2010). Presents an NMR study of what is evidently the unfolded structure of the k-turn in the absence of metal ions. The structure is more extended than the folded one, in agreement with FRET studies. This also accords with a computational study by Sponar and coworkers who observed hinged-like motions in their trajectories, see: Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations. Curuksu J, Sponer J, Zacharias M. Biophys J. 97: 2004-2013 (2009).

January 2010

k-turns in RNA database launched!

 
 
 
Last updated: 16 May 2019, 09:38 AM