4FEJ
Crystal structure of the A24U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine
Summary for 4FEJ
| Entry DOI | 10.2210/pdb4fej/pdb |
| Related | 1U8D 4FE5 4FEL 4FEN 4FEO 4FEP |
| Descriptor | A24U mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain, HYPOXANTHINE, ACETATE ION, ... (5 entities in total) |
| Functional Keywords | three-way junction with distal tertiary interaction, genetic regulatory element, hypoxanthine, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 22865.76 |
| Authors | Stoddard, C.D.,Trausch, J.J.,Widmann, J.,Marcano, J.,Knight, R.,Batey, R.T. (deposition date: 2012-05-30, release date: 2013-02-27, Last modification date: 2024-02-28) |
| Primary citation | Stoddard, C.D.,Widmann, J.,Trausch, J.J.,Marcano-Velazquez, J.G.,Knight, R.,Batey, R.T. Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch. J.Mol.Biol., 425:1596-1611, 2013 Cited by PubMed Abstract: Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs. PubMed: 23485418DOI: 10.1016/j.jmb.2013.02.023 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.5 Å) |
Structure validation
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