3E5E

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

  • 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: 2.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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This is version 1.1 of the entry. See complete history


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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Entity ID: 1
MoleculeChainsLengthOrganismImage
SMK box (SAM-III) Riboswitch for RNAA 53N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.418α = 90
b = 98.418β = 90
c = 86.393γ = 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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Ligand Structure Quality Assessment 



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