Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme.
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.
Jansen
Joshua A
JA
Department of Chemistry, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA.
McCarthy
Tom J
TJ
Soukup
Garrett A
GA
Soukup
Juliane K
JK
D001426:Bacterial Proteins / Q000737:chemistry*; D001483:Base Sequence; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry*; D005945:Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)
D001426:Bacterial Proteins; D008024:Ligands; D008274:Magnesium; D016337:RNA, Catalytic; C000731191:component S, glutamate mutase protein, Bacteria; D005945:Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)