1. Potential contact sites between the protein and RNA subunit in the Bacillus subtilis RNase P holoenzyme.
- Author
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Rox C, Feltens R, Pfeiffer T, and Hartmann RK
- Subjects
- Bacterial Proteins chemistry, Bacterial Proteins genetics, Base Sequence, Binding Sites, Catalytic Domain, Edetic Acid metabolism, Endoribonucleases metabolism, Ferrous Compounds metabolism, Holoenzymes chemistry, Holoenzymes genetics, Holoenzymes metabolism, Iodine metabolism, Models, Molecular, Molecular Sequence Data, Nitrilotriacetic Acid metabolism, Nucleic Acid Conformation, Organometallic Compounds metabolism, Protein Binding, Protein Structure, Tertiary, Protein Subunits, RNA, Bacterial chemistry, RNA, Bacterial genetics, RNA, Catalytic metabolism, RNA-Binding Proteins chemistry, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, Ribonuclease P, Ribonucleoproteins chemistry, Ribonucleoproteins genetics, Ribonucleoproteins metabolism, Bacillus subtilis enzymology, Bacillus subtilis genetics, Bacterial Proteins metabolism, Endoribonucleases chemistry, Endoribonucleases genetics, Nitrilotriacetic Acid analogs & derivatives, RNA, Bacterial metabolism, RNA, Catalytic chemistry, RNA, Catalytic genetics
- Abstract
We have detected by nucleotide analog interference mapping (NAIM) AMPalphaS and IMPalphaS modifications in Bacillus subtilis RNase P RNA that interfere with binding of the homologous protein subunit. Interference as well as some enhancement effects were clustered in two main areas, in P10.1a/L10.1 and P12 of the specificity domain (cluster 1, domain I) and in P2, P3, P15.1, J18/2 and J19/4 of the catalytic domain (cluster 2a, domain II). Minor interferences in P1 and P19 and a strong and weak enhancement effect in P19 represent a third area located in domain II (cluster 2b). Our results suggest that P3, P2-J18/2 and J19/4 are key elements for anchoring of the protein to the catalytic domain close to the scissile phosphodiester in enzyme-substrate complexes. Sites of interference or enhancement in clusters 1 and 2a are located at distances between 65 and 130 A from each other in the current 3D model of a full-length RNase P RNA-substrate complex. Taking into account that the RNase P protein monomer can bridge a maximum distance of about 40 A, simultaneous direct contacts to the two aforementioned potential RNA-binding areas would be incompatible with our current understanding of bacterial RNase P RNA architecture. Our findings suggest that the current 3D model has to be rearranged in order to reduce the distance between clusters 1 and 2a. Alternatively, based on the recent finding that B. subtilis RNase P forms a tetramer consisting of two protein and two RNA subunits, cluster 1 may reflect one protein contact site in domain I, and cluster 2a a separate one in domain II., (Copyright 2002 Academic Press.)
- Published
- 2002
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