Nature Structural & Molecular Biology 13, 517 - 523 (2006)
Published online: 14 May 2006; | doi:10.1038/nsmb1094
Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozymeJoshua A Jansen1, Tom J McCarthy1, Garrett A Soukup2
& Juliane K Soukup11
Department of Chemistry, Creighton University, 2500 California Plaza, Omaha, Nebraska, 68178, USA. 2
Department of Biomedical Sciences, Creighton University School of Medicine, 2500 California Plaza, Omaha, Nebraska, 68178, USA.
Correspondence should be addressed to Garrett A Soukup gasoukup@creighton.edu or Juliane K Soukup jksoukup@creighton.edu The glmS ribozyme resides in the 5' untranslated region of glmS mRNA and functions as a catalytic riboswitch that regulates amino sugar metabolism in certain Gram-positive bacteria. The ribozyme catalyzes self-cleavage of the mRNA and ultimately inhibits gene expression in response to binding of glucosamine-6-phosphate (GlcN6P), the metabolic product of the GlmS protein. We have used nucleotide analog interference mapping (NAIM) and suppression (NAIS) to investigate backbone and nucleobase functional groups essential for ligand-dependent ribozyme function. NAIM using GlcN6P as ligand identified requisite structural features and potential sites of ligand and/or metal ion interaction, whereas NAIS using glucosamine as ligand analog revealed those sites that orchestrate recognition of ligand phosphate. These studies demonstrate that the ligand-binding site lies in close proximity to the cleavage site in an emerging model of ribozyme structure that supports a role for ligand within the catalytic core.
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