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PDBsum entry 2eeu
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dna_rna ligands links
RNA PDB id
2eeu

 

 

 

 

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Contents
DNA/RNA
Ligands
ACT
NCO ×12
HPA
Waters ×212
PDB id:
2eeu
Name: RNA
Title: Guanine riboswitch u22a, a52u mutant bound to hypoxanthine
Structure: Guanine riboswitch. Chain: a. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: this sequence was engineered based on the guanine riboswitch found in the 5'utr of the xpt-pbux gene in bacillus subtilis.
Resolution:
1.95Å     R-factor:   0.232     R-free:   0.275
Authors: S.D.Gilbert,C.E.Love,R.T.Batey
Key ref: S.D.Gilbert et al. (2007). Mutational analysis of the purine riboswitch aptamer domain. Biochemistry, 46, 13297-13309. PubMed id: 17960911
Date:
19-Feb-07     Release date:   13-Nov-07    
 Headers
 References

DNA/RNA chain
  G-G-A-C-A-U-A-A-A-A-U-C-G-C-G-U-G-G-A-U-A-U-G-G-C-A-C-G-C-A-A-G-U-U-U-C-U-U-C- 67 bases

 

 
Biochemistry 46:13297-13309 (2007)
PubMed id: 17960911  
 
 
Mutational analysis of the purine riboswitch aptamer domain.
S.D.Gilbert, C.E.Love, A.L.Edwards, R.T.Batey.
 
  ABSTRACT  
 
The purine riboswitch is one of a number of mRNA elements commonly found in the 5'-untranslated region capable of controlling expression in a cis-fashion via its ability to directly bind small-molecule metabolites. Extensive biochemical and structural analysis of the nucleobase-binding domain of the riboswitch, referred to as the aptamer domain, has revealed that the mRNA recognizes its cognate ligand using an intricately folded three-way junction motif that completely encapsulates the ligand. High-affinity binding of the purine nucleobase is facilitated by a distal loop-loop interaction that is conserved between both the adenine and guanine riboswitches. To understand the contribution of conserved nucleotides in both the three-way junction and the loop-loop interaction of this RNA, we performed a detailed mutagenic survey of these elements in the context of an adenine-responsive variant of the xpt-pbuX guanine riboswitch from Bacillus subtilis. The varying ability of these mutants to bind ligand as measured by isothermal titration calorimetry uncovered the conserved nucleotides whose identity is required for purine binding. Crystallographic analysis of the bound form of five mutants and chemical probing of their free state demonstrate that the identity of several universally conserved nucleotides is not essential for formation of the RNA-ligand complex but rather for maintaining a binding-competent form of the free RNA. These data show that conservation patterns in riboswitches arise from a combination of formation of the ligand-bound complex, promoting an open form of the free RNA, and participating in the secondary structural switch with the expression platform.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21532599 B.Heppell, S.Blouin, A.M.Dussault, J.Mulhbacher, E.Ennifar, J.C.Penedo, and D.A.Lafontaine (2011).
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch.
  Nat Chem Biol, 7, 384-392.  
20961447 J.Grojean, and B.Downes (2010).
Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana.
  Biol Direct, 5, 60.  
20404211 K.S.Keating, and A.M.Pyle (2010).
Semiautomated model building for RNA crystallography using a directed rotameric approach.
  Proc Natl Acad Sci U S A, 107, 8177-8182.  
20108980 M.D.Brenner, M.S.Scanlan, M.K.Nahas, T.Ha, and S.K.Silverman (2010).
Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine.
  Biochemistry, 49, 1596-1605.  
20106958 N.J.Baird, and A.R.Ferré-D'Amaré (2010).
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis.
  RNA, 16, 598-609.  
20022916 V.Delfosse, P.Bouchard, E.Bonneau, P.Dagenais, J.F.Lemay, D.A.Lafontaine, and P.Legault (2010).
Riboswitch structure: an internal residue mimicking the purine ligand.
  Nucleic Acids Res, 38, 2057-2068.
PDB code: 3ivn
19595806 A.D.Garst, and R.T.Batey (2009).
A switch in time: detailing the life of a riboswitch.
  Biochim Biophys Acta, 1789, 584-591.  
19007790 A.L.Edwards, and R.T.Batey (2009).
A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch.
  J Mol Biol, 385, 938-948.
PDB code: 3ds7
19303767 A.Serganov (2009).
The long and the short of riboswitches.
  Curr Opin Struct Biol, 19, 251-259.  
19625387 M.Sharma, G.Bulusu, and A.Mitra (2009).
MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.
  RNA, 15, 1673-1692.  
19741022 M.de la Peña, D.Dufour, and J.Gallego (2009).
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold.
  RNA, 15, 1949-1964.  
19603494 O.Prychyna, M.S.Dahabieh, J.Chao, and M.A.O'Neill (2009).
Sequence-dependent folding and unfolding of ligand-bound purine riboswitches.
  Biopolymers, 91, 953-965.  
19137333 P.Sharma, S.Sharma, M.Chawla, and A.Mitra (2009).
Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches.
  J Mol Model, 15, 633-649.  
19523903 S.D.Gilbert, F.E.Reyes, A.L.Edwards, and R.T.Batey (2009).
Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs.
  Structure, 17, 857-868.
PDB codes: 3fo4 3fo6 3g4m 3gao 3ger 3ges 3gog 3got
19460868 T.H.Chang, H.D.Huang, L.C.Wu, C.T.Yeh, B.J.Liu, and J.T.Horng (2009).
Computational identification of riboswitches based on RNA conserved functional sequences and conformations.
  RNA, 15, 1426-1430.  
18268025 C.D.Stoddard, S.D.Gilbert, and R.T.Batey (2008).
Ligand-dependent folding of the three-way junction in the purine riboswitch.
  RNA, 14, 675-684.  
18495753 T.H.Chang, J.T.Horng, and H.D.Huang (2008).
RNALogo: a new approach to display structural RNA alignment.
  Nucleic Acids Res, 36, W91-W96.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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