4XWF

Crystal structure of the ZMP riboswitch at 1.80 angstrom

Summary for 4XWF

• Entry DOI: 10.2210/pdb4xwf/pdb
• Related: 4XW7
• Descriptor: pfl RNA, AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: rna, riboswitch, zmp, aicar
• Biological source: Actinomyces odontolyticus
• Total number of polymer chains: 1
• Total formula weight: 22508.17

Authors

Trausch, J.J.,Batey, R.T. (deposition date: 2015-01-28, release date: 2015-09-09, Last modification date: 2023-09-27)

Primary citation

Trausch, J.J.,Marcano-Velazquez, J.G.,Matyjasik, M.M.,Batey, R.T.
Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.
Chem.Biol., 22:829-837, 2015

PubMed Abstract: The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP.

PubMed: 26144884
DOI: 10.1016/j.chembiol.2015.06.007

Experimental method

X-RAY DIFFRACTION (1.8 Å)