Identification of catalytic metal ion ligands in ribozymes.
Site-bound metal ions participate in the catalytic mechanisms of many ribozymes. Understanding these mechanisms therefore requires knowledge of the specific ligands on both substrate and ribozyme that coordinate these catalytic metal ions. A number of different structural and biochemical strategies have been developed and refined for identifying metal ion binding sites within ribozymes, and for assessing the catalytic contributions of the metal ions bound at those sites. We review these approaches and provide examples of their application, focusing in particular on metal ion rescue experiments and their roles in the construction of the transition state models for the Tetrahymena group I and RNase P ribozymes.
Frederiksen
John K
JK
The Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA.
Piccirilli
Joseph A
JA
D001703:Biophysics / Q000379:methods; D002384:Catalysis; D018360:Crystallography, X-Ray / Q000379:methods; D030562:Databases, Protein; D007477:Ions; D008024:Ligands; D008670:Metals / Q000737:chemistry*; D008956:Models, Chemical; D008968:Molecular Conformation; D016337:RNA, Catalytic / Q000737:chemistry*; D043262:Ribonuclease P / Q000737:chemistry*; D012984:Software; D013053:Spectrophotometry / Q000379:methods; D055672:Static Electricity; D013768:Tetrahymena / Q000378:metabolism*
D007477:Ions; D008024:Ligands; D008670:Metals; D016337:RNA, Catalytic; D043262:Ribonuclease P