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PDBsum entry 2g9c
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dna_rna ligands links
RNA PDB id
2g9c

 

 

 

 

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Contents
DNA/RNA
Ligands
ACT
NCO ×12
3AY
Waters ×353
PDB id:
2g9c
Name: RNA
Title: Modified pyrimidines specifically bind the purine riboswitch
Structure: Guanine riboswitch. Chain: a. Engineered: yes. Mutation: yes. Other_details: adenine responsive mutant guanine riboswitch
Source: Synthetic: yes. Other_details: this sequence was engineered based on the guanine riboswitch from the xpt-pbux gene in bacillus subtilis
Resolution:
1.70Å     R-factor:   0.195     R-free:   0.242
Authors: S.D.Gilbert,S.J.Mediatore,R.T.Batey
Key ref: S.D.Gilbert et al. (2006). Modified pyrimidines specifically bind the purine riboswitch. J Am Chem Soc, 128, 14214-14215. PubMed id: 17076468 DOI: 10.1021/ja063645t
Date:
06-Mar-06     Release date:   21-Nov-06    
 Headers
 References

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

 

 
DOI no: 10.1021/ja063645t J Am Chem Soc 128:14214-14215 (2006)
PubMed id: 17076468  
 
 
Modified pyrimidines specifically bind the purine riboswitch.
S.D.Gilbert, S.J.Mediatore, R.T.Batey.
 
  ABSTRACT  
 
The purine riboswitch is a genetic regulatory element found in the 5'-untranslated regions of Gram-positive bacteria that regulates expression of the mRNA specifically in response to either guanine or adenine. We report that the adenine-responsive RNA element is also capable of specifically recognizing pyrimidine compounds bearing modifications at the 6- or 5,6-positions in a fashion similar to that of purine compounds. Using isothermal titration calorimetry and X-ray crystallography, the binding of these compounds is characterized.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21439477 P.Daldrop, F.E.Reyes, D.A.Robinson, C.M.Hammond, D.M.Lilley, R.T.Batey, and R.Brenk (2011).
Novel ligands for a purine riboswitch discovered by RNA-ligand docking.
  Chem Biol, 18, 324-335.
PDB codes: 2xnw 2xnz 2xo0 2xo1
20421948 J.Mulhbacher, E.Brouillette, M.Allard, L.C.Fortier, F.Malouin, and D.A.Lafontaine (2010).
Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways.
  PLoS Pathog, 6, e1000865.  
20133756 N.Dixon, J.N.Duncan, T.Geerlings, M.S.Dunstan, J.E.McCarthy, D.Leys, and J.Micklefield (2010).
Reengineering orthogonally selective riboswitches.
  Proc Natl Acad Sci U S A, 107, 2830-2835.
PDB code: 3la5
20026131 U.D.Priyakumar, and A.D.MacKerell (2010).
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.
  J Mol Biol, 396, 1422-1438.  
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
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
18835447 N.N.Salim, and A.L.Feig (2009).
Isothermal titration calorimetry of RNA.
  Methods, 47, 198-205.  
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
17671974 A.L.Feig (2007).
Applications of isothermal titration calorimetry in RNA biochemistry and biophysics.
  Biopolymers, 87, 293-301.  
17989489 G.Portalone, and M.Colapietro (2007).
Hydrogen-bonded supramolecular motifs in the 1:1 monohydrated molecular adduct of acetoguanaminium chloride with acetoguanamine and in 2,4,6-triaminopyrimidinediium dichloride dihydrate.
  Acta Crystallogr C, 63, o655-o658.  
17704135 J.Mulhbacher, and D.A.Lafontaine (2007).
Ligand recognition determinants of guanine riboswitches.
  Nucleic Acids Res, 35, 5568-5580.  
17960911 S.D.Gilbert, C.E.Love, A.L.Edwards, and R.T.Batey (2007).
Mutational analysis of the purine riboswitch aptamer domain.
  Biochemistry, 46, 13297-13309.
PDB codes: 2ees 2eet 2eeu 2eev 2eew
17574837 T.E.Edwards, D.J.Klein, and A.R.Ferré-D'Amaré (2007).
Riboswitches: small-molecule recognition by gene regulatory RNAs.
  Curr Opin Struct Biol, 17, 273-279.  
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 codes are shown on the right.

 

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