2OEU image
Deposition Date 2007-01-01
Release Date 2007-02-20
Last Version Date 2023-08-30
Entry Detail
PDB ID:
2OEU
Keywords:
Title:
Full-length hammerhead ribozyme with Mn(II) bound
Biological Source:
Source Organism:
(Taxon ID: )
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.22
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:Hammerhead Ribozyme
Chain IDs:A
Chain Length:43
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule: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'
Chain IDs:B
Chain Length:20
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5BU B U 5-BROMO-URIDINE-5'-MONOPHOSPHATE
GTP A G GUANOSINE-5'-TRIPHOSPHATE
OMC B C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
Ligand Molecules
Primary Citation
Solvent structure and hammerhead ribozyme catalysis.
Chem.Biol. 15 332 342 (2008)
PMID: 18420140 DOI: 10.1016/j.chembiol.2008.03.010

Abstact

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.

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Primary Citation of related structures