3DS7

Structure of an RNA-2'-deoxyguanosine complex

Summary for 3DS7

• Entry DOI: 10.2210/pdb3ds7/pdb
• Descriptor: 67-MER, ACETATE ION, COBALT HEXAMMINE(III), ... (5 entities in total)
• Functional Keywords: rna, rna-ligand complex, riboswitch
• Total number of polymer chains: 2
• Total formula weight: 45510.59

Authors

Edwards, A.L.,Batey, R.T. (deposition date: 2008-07-11, release date: 2009-02-17, Last modification date: 2023-08-30)

Primary citation

Edwards, A.L.,Batey, R.T.
A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch.
J.Mol.Biol., 385:938-948, 2009

PubMed Abstract: Riboswitches are noncoding RNA elements that are commonly found in the 5'-untranslated region of bacterial mRNA. Binding of a small-molecule metabolite to the riboswitch aptamer domain guides the folding of the downstream sequence into one of two mutually exclusive secondary structures that directs gene expression. The purine riboswitch family, which regulates aspects of purine biosynthesis and transport, contains three distinct classes that specifically recognize guanine/hypoxanthine, adenine, or 2'-deoxyguanosine (dG). Structural analysis of the guanine and adenine classes revealed a binding pocket that almost completely buries the nucleobase within the core of the folded RNA. Thus, it is somewhat surprising that this family of RNA elements also recognizes dG. We have used a combination of structural and biochemical techniques to understand how the guanine riboswitch could be converted into a dG binder and the structural basis for dG recognition. These studies reveal that a limited number of sequence changes to a guanine-sensing RNA are required to cause a specificity switch from guanine to 2'-deoxyguanosine, and to impart an altered structure for accommodating the additional deoxyribose sugar moiety.

PubMed: 19007790
DOI: 10.1016/j.jmb.2008.10.074

Experimental method

X-RAY DIFFRACTION (1.85 Å)