PDBsum entry 3e5c

RNA

PDB id: 3e5c

Contents

DNA/RNA

Ligands

SAM

Metals

_SR ×15

Waters ×69

PDB id:

3e5c

Name:

RNA

Title:

Crystal structure of the smk box (sam-iii) riboswitch with sam

Structure:

Smk box (sam-iii) riboswitch. Chain: a. Engineered: yes

Source:

Synthetic: yes. Other_details: RNA was prepared by in vitro transcription

Resolution:

2.25Å R-factor: 0.221 R-free: 0.227

Authors:

C.Lu

Key ref:

C.Lu et al. (2008). Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat Struct Biol, 15, 1076-1083. PubMed id: 18806797 DOI: 10.1038/nsmb.1494

Date:

13-Aug-08 Release date: 07-Oct-08

DNA/RNA chain

GTP-U-U-C-C-C-G-A-A-A-G-G-A-U-G-G-C-G-G-A-A-A-C-G-C-C-A-G-A-U-G-C-C-U-U-G-U-A- 53 bases

DOI no: 10.1038/nsmb.1494

Nat Struct Biol 15:1076-1083 (2008)

PubMed id: 18806797

Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.

C.Lu, A.M.Smith, R.T.Fuchs, F.Ding, K.Rajashankar, T.M.Henkin, A.Ke.

ABSTRACT

Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The S(MK) box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-A crystal structure of the Enterococcus faecalis S(MK) box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti-Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the S(MK) box riboswitch sampling the near-cognate ligand S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.

Selected figure(s)

Figure 3.
The labeling and base coloring scheme are consistent with that in Figure 1. (a) Stereo view of the SAM binding site in the S[MK] box riboswitch. The adenosine moiety of SAM is shown to base-stack between U72 and G90. (b) The A73 circle G90-C35 base triple paves the 'floor' of the SAM binding pocket. The C-G base pair is co-planar, whereas A73 contacts from the minor groove of G90 at a 45° tilted angle, which orients N6 of A73 for SAM recognition one base plane above.

Figure 4.
(a) Stereo view of the binding pocket in the S[MK] box riboswitch in complex with Se-SAM. The location of the selenium atom is confirmed by the strong anomalous-difference density shown in blue contoured at 8 . The rest of the binding pocket in the Se-SAM–bound S[MK] structure is almost identical to that in the SAM-bound structure. Magenta mesh signifies the simulated composite omit electron-density map of Se-SAM contoured at 1.5 . (b) Stereo view of the SAH-bound S[MK] structure from a direction similar to that shown in a. The simulated annealing omit map contoured at 0.8 level clearly shows that the ribose and sulfide moieties rotate 180° to exit the RNA from the linker helix side.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 1076-1083) copyright 2008.

Figures were selected by an automated process.