4L81

Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for diversity in the SAM clan of riboswitches.

Trausch, J.J.Xu, Z.Edwards, A.L.Reyes, F.E.Ross, P.E.Knight, R.Batey, R.T.

(2014) Proc Natl Acad Sci U S A 111: 6624-6629

  • DOI: 10.1073/pnas.1312918111
  • Primary Citation of Related Structures:  
    4L81, 4OQU

  • PubMed Abstract: 
  • In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery ...

    In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO, 80309-0596.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
SAM-I/IV variant riboswitch aptamer domainA96N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.93α = 90
b = 120.93β = 90
c = 186.56γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release