4ZNP

The structure of A pfI Riboswitch Bound to ZMP

Summary for 4ZNP

• Entry DOI: 10.2210/pdb4znp/pdb
• Descriptor: pfI Riboswitch, AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: zmp, riboswitch, rna, one carbon mechanism, aicar, ztp, complex
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 48167.77

Authors

Ren, A.,Patel, D.J.,Rajashankar, R.K. (deposition date: 2015-05-05, release date: 2015-08-26, Last modification date: 2024-03-06)

Primary citation

Ren, A.,Rajashankar, K.R.,Patel, D.J.
Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.
Structure, 23:1375-1381, 2015

PubMed Abstract: ZTP, the pyrophosphorylated analog of ZMP (5-amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. We report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines, while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg(2+), contrasts with exposure of the 5'-phosphate to solvent. Our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.

PubMed: 26118534
DOI: 10.1016/j.str.2015.05.016

Experimental method

X-RAY DIFFRACTION (2.94 Å)