3PDR

Crystal structure of manganese bound M-box RNA

Summary for 3PDR

• Entry DOI: 10.2210/pdb3pdr/pdb
• Descriptor: M-box Riboswitch RNA, POTASSIUM ION, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: manganese-rna complex, rna
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 105229.45

Authors

Ramesh, A.,Winkler, W.C. (deposition date: 2010-10-23, release date: 2011-02-23, Last modification date: 2024-02-21)

Primary citation

Ramesh, A.,Wakeman, C.A.,Winkler, W.C.
Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes.
J.Mol.Biol., 407:556-570, 2011

PubMed Abstract: The M-box riboswitch couples intracellular magnesium levels to expression of bacterial metal transport genes. Structural analyses on other riboswitch RNA classes, which typically respond to a small organic metabolite, have revealed that ligand recognition occurs through a combination of base-stacking, electrostatic, and hydrogen-bonding interactions. In contrast, the M-box RNA triggers a change in gene expression upon association with an undefined population of metals, rather than responding to only a single ligand. Prior biophysical experimentation suggested that divalent ions associate with the M-box RNA to promote a compacted tertiary conformation, resulting in sequestration of a short sequence tract otherwise required for downstream gene expression. Electrostatic shielding from loosely associated metals is undoubtedly an important influence during this metal-mediated compaction pathway. However, it is also likely that a subset of divalent ions specifically occupies cation binding sites and promotes proper positioning of functional groups for tertiary structure stabilization. To better elucidate the role of these metal binding sites, we resolved a manganese-chelated M-box RNA complex to 1.86 Å by X-ray crystallography. These data support the presence of at least eight well-ordered cation binding pockets, including several sites that had been predicted by biochemical studies but were not observed in prior structural analysis. Overall, these data support the presence of three metal-binding cores within the M-box RNA that facilitate a network of long-range interactions within the metal-bound, compacted conformation.

PubMed: 21315082
DOI: 10.1016/j.jmb.2011.01.049

Experimental method

X-RAY DIFFRACTION (1.853 Å)