5C7W

5'-monophosphate Z:P Guanine Riboswitch bound to hypoxanthine.

Summary for 5C7W

• Entry DOI: 10.2210/pdb5c7w/pdb
• Descriptor: 5'-monophosphate Z:P guanine riboswitch, COBALT HEXAMMINE(III), HYPOXANTHINE (3 entities in total)
• Functional Keywords: expanded rna; riboswitch; unnatural base pair, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 22975.83

Authors

Hernandez, A.R.,Shao, Y.,Hoshika, S.,Yang, Z.,Shelke, S.A.,Herrou, J.,Kim, H.-J.,Kim, M.-J.,Piccirilli, J.A.,Benner, S.A. (deposition date: 2015-06-25, release date: 2015-08-12, Last modification date: 2024-05-01)

Primary citation

Hernandez, A.R.,Shao, Y.,Hoshika, S.,Yang, Z.,Shelke, S.A.,Herrou, J.,Kim, H.J.,Kim, M.J.,Piccirilli, J.A.,Benner, S.A.
A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.
Angew.Chem.Int.Ed.Engl., 54:9853-9856, 2015

PubMed Abstract: As one of its goals, synthetic biology seeks to increase the number of building blocks in nucleic acids. While efforts towards this goal are well advanced for DNA, they have hardly begun for RNA. Herein, we present a crystal structure for an RNA riboswitch where a stem C:G pair has been replaced by a pair between two components of an artificially expanded genetic-information system (AEGIS), Z and P, (6-amino-5-nitro-2(1H)-pyridone and 2-amino-imidazo[1,2-a]-1,3,5-triazin-4-(8H)-one). The structure shows that the Z:P pair does not greatly change the conformation of the RNA molecule nor the details of its interaction with a hypoxanthine ligand. This was confirmed in solution by in-line probing, which also measured a 3.7 nM affinity of the riboswitch for guanine. These data show that the Z:P pair mimics the natural Watson-Crick geometry in RNA in the first example of a crystal structure of an RNA molecule that contains an orthogonal added nucleobase pair.

PubMed: 26223188
DOI: 10.1002/anie.201504731

Experimental method

X-RAY DIFFRACTION (3.22 Å)