4FE5

Crystal structure of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine

Replaces:  1U8D

Summary for 4FE5

• Entry DOI: 10.2210/pdb4fe5/pdb
• Related: 4FEJ 4FEL 4FEN 4FEO 4FEP
• Descriptor: xpt-pbuX guanine riboswitch aptamer domain, HYPOXANTHINE, ACETATE ION, ... (5 entities in total)
• Functional Keywords: three-way junction with distal tertiary interaction, gene regulatory element, hypoxanthine, rna
• Total number of polymer chains: 1
• Total formula weight: 22727.68

Authors

Stoddard, C.D.,Trausch, J.J.,Widmann, J.,Marcano, J.,Knight, R.,Batey, R.T. (deposition date: 2012-05-29, release date: 2012-06-27, Last modification date: 2024-02-28)

Primary citation

Batey, R.T.,Gilbert, S.D.,Montange, R.K.
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.
Nature, 432:411-415, 2004

PubMed Abstract: Riboswitches are genetic regulatory elements found in the 5' untranslated region of messenger RNA that act in the absence of protein cofactors. They are broadly distributed across bacteria and account for the regulation of more than 2% of all genes in Bacillus subtilis, underscoring their importance in the control of cellular metabolism. The 5' untranslated region of many mRNAs of genes involved in purine metabolism and transport contain a guanine-responsive riboswitch that directly binds guanine, hypoxanthine or xanthine to terminate transcription. Here we report the crystal structure at 1.95 A resolution of the purine-binding domain of the guanine riboswitch from the xpt-pbuX operon of B. subtilis bound to hypoxanthine, a prevalent metabolite in the bacterial purine salvage pathway. This structure reveals a complex RNA fold involving several phylogenetically conserved nucleotides that create a binding pocket that almost completely envelops the ligand. Hypoxanthine functions to stabilize this structure and to promote the formation of a downstream transcriptional terminator element, thereby providing a mechanism for directly repressing gene expression in response to an increase in intracellular concentrations of metabolite.

PubMed: 15549109
DOI: 10.1038/nature03037

Experimental method

X-RAY DIFFRACTION (1.32 Å)