1. Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent.
- Author
-
Westhof E, Wesolowski D, and Altman S
- Subjects
- Bacterial Proteins chemistry, Bacterial Proteins metabolism, Base Sequence, Coenzymes drug effects, Computer Simulation, Endoribonucleases drug effects, Escherichia coli chemistry, Magnesium pharmacology, Models, Molecular, Molecular Sequence Data, Protein Binding, RNA, Bacterial drug effects, RNA, Catalytic drug effects, RNA, Transfer chemistry, RNA, Transfer metabolism, Ribonuclease P, Coenzymes chemistry, Edetic Acid pharmacology, Endoribonucleases chemistry, Escherichia coli Proteins, Ferrous Compounds pharmacology, Nucleic Acid Conformation, RNA, Bacterial chemistry, RNA, Catalytic chemistry
- Abstract
The accessibility of the ribose groups in the phosphodiester chain of M1 RNA, the catalytic subunit of ribonuclease P from Escherichia coli, has been probed with an Fe(II)-EDTA reagent when the RNA is alone in solution, when it is in a complex with a tRNA precursor substrate, and when it is in the holoenzyme complex with its cofactor, C5 protein. The regions found to be protected under these various conditions, as well as those previously identified in other chemical probing experiments, have been mapped on a three-dimensional working model of M1 RNA and are generally compatible with the previously proposed placement of the substrate on the enzyme and with previous data and inferences regarding the interactions of C5 protein with M1 RNA. On the basis of the accessibilities of the C(4') atoms, refinements have been introduced in the model to accommodate the Fe(II)-EDTA protection data. The protein cofactor makes contact with several helical regions of the catalytic RNA on the opposite side of the surface to which substrates bind.
- Published
- 1996
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