RNA Structure: Roles of Divalent Metal Ions

Richard J Carter, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Stephen R Holbrook, Lawrence Berkeley National Laboratory, Berkeley, California, USA

Published online: February 2003

DOI: 10.1038/npg.els.0003136

Divalent metal ions play an important role in charge neutralization and incorrectly folding RNA into its three-dimensional structure. They also play a potentially important role in the catalytic activity of RNA.

Keywords: RNA; divalent metal ions; catalysis; structure and folding; thermodynamics

Figure 1. The high-resolution crystal structure of transfer RNA and bound divalent metal ions. The sites that can bind magnesium are shown in blue, the site that can bind cobalt or magnesium is shown in orange, the site that can bind magnesium, manganese or cobalt is shown in magenta and the site that binds magnesium, manganese, zinc, cobalt or lead is shown in yellow.
Figure 2. The four possible modes of RNA catalysis using divalent metal ions. (a) General base catalysis; (b) Lewis acid (electrophilic) catalysis; (c) leaving group activation; (d) nucleophilic activation.
Figure 3. The crystal structure of the P5–P6 domain of the Tetrahymena thermophila group I intron showing the magnesium core. (The magenta sites are cobalt hexamine sites in the crystal structure, which are analogous to hexahydrated magnesium.)
close
 References
    Cate JH, Gooding AR, Podell E et al. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science273: 1678–1685.
    Correll CC, Freeborn B, Moore PB and Steitz TA (1997) Metals, motifs and recognition in the crystal structure of a 5S rRNA domain. Cell91: 705–712.
    Gonzales RLJ and Tinoco IJ (1999) Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot. Journal of Molecular Biology289: 1267–1282.
    Kim S-H, Suddath FL, Quigley GJ et al. (1974) Three-dimensional structure of yeast phenylalanine transfer RNA. Science185: 435–440.
    Oh B-K, Frank DN and Pace NR (1998) Participation of the 3¢-CCA of tRNA in the binding of catalytic  Mg2+ions by ribonuclease P. Biochemistry37: 7277–7283.
    Perotta AT, Shih I and Been MD (1999) Imidazole rescue of a cytosine mutation in a self cleaving ribozyme. Science286: 123–126.
    Robertus JD, Ladner JE, Finch JT et al. (1974) Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature250: 546–551.
    Scott WG, Murray JB, Arnold JRP, Stoddard BL and Klug A (1996) Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science274: 2065–2069.
    Shi H and Moore PB (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA6: 1091–1105.
    Young KJ, Gill F and Grasby JA (1997) Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Research25(19): 3760–3766.
 Further Reading
    book Gesteland RF, Cech TR and Atkins JF (eds)(1993) The RNA World,2nd edn.New York: Cold Spring Harbor Press.
    book Gesteland RF and Atkins JF (eds)(1999) The RNA World. New York: Cold Spring Harbor Press.
    Hanna R and Doudna JA (2000) Metal ions in ribozyme folding and catalysis. Current Opinion in Chemical Biology4: 166–170.
    ePath Nucleic Acid Database (NDB)(2001)[ http://ndbserver.rutgers.edu ]
    ePath Protein Data Bank (PDB) (2001)[ http://www.rcsb.org/pdb/index.html ]
    Tinoco I Jr and Bustamante C (1999) How RNA Folds. Journal of Molecular Biology293: 271–281.

Related Sub-Topics:

Nucleic Acid Structure | RNA Structure and Function | Biomolecular Interactions | Enzymes: Structure and Action Mechanism | Nucleic Acids: Structure, Function, Metabolism
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: RNA Structure: Roles of Divalent Metal Ions
 
How to Cite close
Carter, Richard J, and Holbrook, Stephen R(Feb 2003) RNA Structure: Roles of Divalent Metal Ions. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0003136]