3E5F

Crystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2008-08-13 Released: 2008-10-07 
  • Deposition Author(s): Lu, C.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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Literature

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

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

(2008) Nat Struct Mol Biol 15: 1076-1083

  • DOI: 10.1038/nsmb.1494
  • Primary Citation of Related Structures:  
    3E5C, 3E5E, 3E5F

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

    Department of Molecular Biology and Genetics, Cornell University, 251 Biotechnology Building, Ithaca, New York 14853, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
SMK box (SAM-III) Riboswitch for RNAA 53N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EEM
Query on EEM
Download Ideal Coordinates CCD File 
Q [auth A][(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium
C15 H23 N6 O5 Se
GGJFWMOVUFBSIN-FCKMPRQPSA-O		 Ligand Interaction
SR
Query on SR
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.776α = 90
b = 96.776β = 90
c = 86.765γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-08-13 
  • Released Date: 2008-10-07 
    • Deposition Author(s): Lu, C.

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance