Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?

We have constructed a model structure that we believe represents the strong est possible physically and chemically reasonable representation of a hypot hesized catalytically active hammerhead ribozyme structure in which a singl e divalent metal ion bridges the A9 and scissile phosphate groups. It has b een proposed that such a structure arises from a conformational change in w hich the so-called ground-state structure (as observed by X-ray crystallogr aphy) rearranges in such a way that the pro-R oxygen atoms of both the A9 a nd scissile phosphate groups are directly coordinated by a single divalent metal ion in the transition-state of the hammerhead ribozyme cleavage react ion. We show that even the small subset of possible model structures that a re consistent with these requirements, and that are stereochemically and st erically reasonable, are contradicted by experimental evidence. We also dem onstrate that even a minimal subset of assumptions, i.e. that stems I and I I are helical and that the two phosphate groups are coordinated by a divale nt metal ion in the standard octahedral geometry, are sufficient to lead to this contradiction. We therefore conclude that such a mechanism of hammerh ead ribozyme catalysis is untenable, at least in its present formulation. ( C) 2000 Academic Press.