Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain

Abstract

Two new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 A, respectively. This loop E region is distorted by three "cross-strand purine stacks" and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface.

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

“…The S-shape of strand 1 is not present in the fragment crystal structure of isolated 5S rRNA loop E in url064/354D (Correll et al 1997). However, the dented stack switch of 1e survives in the fragment, with an additional 1e now seen on strand 1; the region between the two 1e stack-switches has noncanonical base pairs, in a trans rather than the usual cis relationship.…”

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg2+ Binding Site is Located Close to the Stacked Branch Adenosine

“…As proposed by fluorescence studies [28] of a tetraloop structure, it is well feasible that two Mg 2+ ions bind in close proximity at this site, even though one could also picture one Mg 2+ ion "rolling" over the whole tetraloop region. Indeed, it has been shown before that nucleic acids can accommodate two metal ions in surprisingly close neighborhood to each other, [29,30] and that their binding affinity is hardly affected. [30] Taken together, the accumulated data from out Mg 2+ titration studies reveal the following with similar affinities (a detailed evaluation of the affinity constants within D6-27 will be published elsewhere).…”

Protonated 2‘-Aminoguanosine as a Probe of the Electrostatic Environment of the Active Site of the Tetrahymena Group I Ribozyme

“…We therefore use the simpler model in which a single Mg 2+ ion weakens the binding of G NH 3 + (Scheme 4). 6 Analysis of the data of Figure 5B according to the model of Scheme 4 allowed estimation of limits for the individual equilibrium constants. The binding of G NH 3 + continues to increase at the lowest Mg 2+ concentrations; thus, the value of 1000 mM -1 observed at 2 mM Mg 2+ represents a lower limit for the binding of G NH (1).…”

“…The backbone of RNA is composed of negatively charged phosphoryl groups; this results in repulsive interactions, but also creates numerous potential binding sites for metal ions and other positively charged groups (e.g., 2-15 and references cited therein). The 2′-hydroxyl groups and functional groups on the bases of RNA also provide hydrogen bond donors and acceptors that can interact with each other, with metal ions, and with polar groups on bound ligands (e.g., 3,4,6,8,9,[11][12][13][14][16][17][18][19][20][21], and references cited therein). The ring moieties of the bases are nonpolar, creating the potential for hydrophobic interactions with each other and with bound ligands (e.g., 19, 21, and references cited therein).…”