2OEU

Full-length hammerhead ribozyme with Mn(II) bound

Summary for 2OEU

• Entry DOI: 10.2210/pdb2oeu/pdb
• Related: 2goz
• Descriptor: Hammerhead Ribozyme, 5'-R(*GP*GP*CP*GP*UP*(OMC)P*CP*UP*GP*GP*(5BU)P*AP*UP*CP*CP*AP*AP*UP*CP*(DC))-3', MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: ribozyme, hammerhead rna, stem-loop interaction, uridine turn, a-form helix, manganese, mn, rna
• Total number of polymer chains: 2
• Total formula weight: 20708.71

Authors

Martick, M.,Scott, W.G. (deposition date: 2007-01-01, release date: 2007-02-20, Last modification date: 2023-08-30)

Primary citation

Martick, M.,Lee, T.S.,York, D.M.,Scott, W.G.
Solvent structure and hammerhead ribozyme catalysis.
Chem.Biol., 15:332-342, 2008

PubMed Abstract: Although the hammerhead ribozyme is regarded as a prototype for understanding RNA catalysis, the mechanistic roles of associated metal ions and water molecules in the cleavage reaction remain controversial. We have investigated the catalytic potential of observed divalent metal ions and water molecules bound to a 2 A structure of the full-length hammerhead ribozyme by using X-ray crystallography in combination with molecular dynamics simulations. A single Mn(2+) is observed to bind directly to the A9 phosphate in the active site, accompanying a hydrogen-bond network involving a well-ordered water molecule spanning N1 of G12 (the general base) and 2'-O of G8 (previously implicated in general acid catalysis) that we propose, based on molecular dynamics calculations, facilitates proton transfer in the cleavage reaction. Phosphate-bridging metal interactions and other mechanistic hypotheses are also tested with this approach.

PubMed: 18420140
DOI: 10.1016/j.chembiol.2008.03.010

Experimental method

X-RAY DIFFRACTION (2 Å)