2b57

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spinqualitylabelsall models 2b57, resolution 2.15Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Guanine Riboswitch C74U mutant bound to 2,6-diaminopurine

Overview

Riboswitches are cis-acting genetic regulatory elements found commonly in, bacterial mRNAs that consist of a metabolite-responsive aptamer domain, coupled to a regulatory switch. Purine riboswitches respond to, intracellular concentrations of either adenine or guanine/hypoxanthine to, control gene expression. The aptamer domain of the purine riboswitch, contains a pyrimidine residue (Y74) that forms a Watson-Crick base-pairing, interaction with the bound purine nucleobase ligand that discriminates, between adenine and guanine. We sought to understand the structural basis, of this specificity and the mechanism of ligand recognition by the purine, riboswitch. Here, we present the 2,6-diaminopurine-bound structure of a, C74U mutant of the xpt-pbuX guanine riboswitch, along with a detailed, thermodynamic and kinetic analysis of nucleobase recognition by both the, native and mutant riboswitches. These studies demonstrate clearly that the, pyrimidine at position 74 is the sole determinant of purine riboswitch, specificity. In addition, the mutant riboswitch binds adenine and adenine, derivatives well compared with the guanine-responsive riboswitch. Under, our experimental conditions, 2,6-diaminopurine binds the RNA with, DeltaH=-40.3 kcal mol(-1), DeltaS=-97.6 cal mol(-1)K(-1), and, DeltaG=-10.73 kcal mol(-1). A kinetic determination of the slow rate (0.15, x 10(5)M(-1)s(-1) and 2.1 x 10(5)mM(-1)s(-1) for 2-aminopurine binding the, adenine-responsive mutant riboswitch and 7-deazaguanine-binding guanine, riboswitch, respectively) of association under varying experimental, conditions allowed us to propose a mechanism for ligand recognition by the, purine riboswitch. A conformationally dynamic unliganded state for the, binding pocket is stabilized first by the Watson-Crick base pairing, between the ligand and Y74, and by the subsequent ordering of the J2/3, loop, enclosing the ligand within the three-way junction.

About this Structure

2B57 is a Single protein structure of sequence from [1] with , and as ligands. Full crystallographic information is available from OCA.

Reference

Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain., Gilbert SD, Stoddard CD, Wise SJ, Batey RT, J Mol Biol. 2006 Jun 9;359(3):754-68. Epub 2006 Apr 21. PMID:16650860

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