Summary for 4KQY
| Entry DOI | 10.2210/pdb4kqy/pdb |
| Descriptor | YitJ S box/SAM-I riboswitch, S-ADENOSYLMETHIONINE, MAGNESIUM ION, ... (4 entities in total) |
| Functional Keywords | gene regulation, rna |
| Biological source | Bacillus subtilis |
| Total number of polymer chains | 1 |
| Total formula weight | 39019.19 |
| Authors | |
| Primary citation | Lu, C.,Ding, F.,Chowdhury, A.,Pradhan, V.,Tomsic, J.,Holmes, W.M.,Henkin, T.M.,Ke, A. SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch J.Mol.Biol., 404:803-818, 2010 Cited by PubMed Abstract: S-box (SAM-I) riboswitches are a widespread class of riboswitches involved in the regulation of sulfur metabolism in Gram-positive bacteria. We report here the 3.0-Å crystal structure of the aptamer domain of the Bacillus subtilis yitJ S-box (SAM-I) riboswitch bound to S-adenosyl-L-methionine (SAM). The RNA folds into two sets of helical stacks spatially arranged by tertiary interactions including a K-turn and a pseudoknot at a four-way junction. The tertiary structure is further stabilized by metal coordination, extensive ribose zipper interactions, and SAM-mediated tertiary interactions. Despite structural differences in the peripheral regions, the SAM-binding core of the B. subtilis yitJ riboswitch is virtually superimposable with the previously determined Thermoanaerobacter tengcongensis yitJ riboswitch structure, suggesting that a highly conserved ligand-recognition mechanism is utilized by all S-box riboswitches. SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing analysis further revealed that the alternative base-pairing element in the expression platform controls the conformational switching process. In the absence of SAM, the apo yitJ aptamer domain folds predominantly into a pre-binding conformation that resembles, but is not identical with, the SAM-bound state. We propose that SAM enters the ligand-binding site through the "J1/2-J3/4" gate and "locks" down the SAM-bound conformation through an induced-fit mechanism. Temperature-dependent SHAPE revealed that the tertiary interaction-stabilized SAM-binding core is extremely stable, likely due to the cooperative RNA folding behavior. Mutational studies revealed that certain modifications in the SAM-binding region result in loss of SAM binding and constitutive termination, which suggests that these mutations lock the RNA into a form that resembles the SAM-bound form in the absence of SAM. PubMed: 20951706DOI: 10.1016/j.jmb.2010.09.059 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.02 Å) |
Structure validation
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