3SKR: Crystal Structure Of The 2'- Deoxyguanosine Riboswitch Bound To 2'- Deoxyguanosine, Cobalt Hexammine Soak

Citation:
Abstract
Purine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles that define dG selectivity, we determined crystal structures of the natural Mesoplasma florum riboswitch bound to cognate dG as well as to noncognate guanosine, deoxyguanosine monophosphate and guanosine monophosphate. Comparison with related purine riboswitch structures reveals that the dG riboswitch achieves its specificity through modification of key interactions involving the nucleobase and rearrangement of the ligand-binding pocket to accommodate the additional sugar moiety. In addition, we observe new conformational changes beyond the junctional binding pocket extending as far as peripheral loop-loop interactions. It appears that re-engineering riboswitch scaffolds will require consideration of selectivity features dispersed throughout the riboswitch tertiary fold, and structure-guided drug design efforts targeted to junctional RNA scaffolds need to be addressed within such an expanded framework.
PDB ID: 3SKRDownload
MMDB ID: 92768
PDB Deposition Date: 2011/6/23
Updated in MMDB: 2011/10
Experimental Method:
x-ray diffraction
Resolution: 3.1  Å
Biological Unit for 3SKR: monomeric; determined by author
Molecular Components in 3SKR
Label Count Molecule
Nucleotide(1 molecule)
1
RNA (66-mer)
Molecule annotation
Chemicals (8 molecules)
1
1
2
5
3
2
* Click molecule labels to explore molecular sequence information.

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