6P2H

Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches

Summary for 6P2H

• Entry DOI: 10.2210/pdb6p2h/pdb
• Descriptor: RNA (69-MER), 2'-DEOXY-GUANOSINE, COBALT HEXAMMINE(III), ... (5 entities in total)
• Functional Keywords: riboswitch aptamer 2'-deoxyguanosine purine nucleoside, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 23517.53

Authors

Matyjasik, M.M.,Batey, R.T. (deposition date: 2019-05-21, release date: 2019-10-23, Last modification date: 2023-10-11)

Primary citation

Matyjasik, M.M.,Batey, R.T.
Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches.
Nucleic Acids Res., 47:10931-10941, 2019

PubMed Abstract: A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the regulatory molecule of the parental class. Within the guanine/adenine class, seven groups of RNAs were identified that deviate from the consensus sequence at one or more of three positions directly involved purine nucleobase recognition, one of which was validated as a second class of 2'-deoxyguanosine riboswitch (called 2'-dG-II). To understand how 2'-dG-II riboswitches recognize their cognate ligand and how they differ from a previously identified class of 2'-deoxyguanosine binding riboswitches, we have solved the crystal structure of a 2'-dG-II aptamer domain bound to 2'-deoxyguanosine. This structure reveals a global architecture similar to other members of the purine riboswitch family, but contains key differences within the ligand binding core. Defining the 2'-dG-II riboswitches is a two-nucleotide insertion in the three-way junction that promotes novel base-base interactions. Unlike 2'-dG-I riboswitches, the 2'-dG-II class only requires local changes to the ligand binding pocket of the guanine/adenine class to achieve a change in ligand preference. Notably, members of the 2'-dG-II family have variable ability to discriminate between 2'-deoxyguanosine and riboguanosine, suggesting that a subset of 2'-dG-II riboswitches may bind either molecule to regulate gene expression.

PubMed: 31598729
DOI: 10.1093/nar/gkz839

Experimental method

X-RAY DIFFRACTION (2.803 Å)