Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme.
Bacterial ribonuclease P (RNase P), an enzyme involved in tRNA maturation, consists of a catalytic RNA subunit and a protein cofactor. Comparative phylogenetic analysis and molecular modeling have been employed to derive secondary and tertiary structure models of the RNA subunits from Escherichia coli (type A) and Bacillus subtilis (type B) RNase P. The tertiary structure of the protein subunit of B.subtilis and Staphylococcus aureus RNase P has recently been determined. However, an understanding of the structure of the RNase P holoenzyme (i.e. the ribonucleoprotein complex) is lacking. We have now used an EDTA-Fe-based footprinting approach to generate information about RNA-protein contact sites in E.coli RNase P. The footprinting data, together with results from other biochemical and biophysical studies, have furnished distance constraints, which in turn have enabled us to build three-dimensional models of both type A and B versions of the bacterial RNase P holoenzyme in the absence and presence of its precursor tRNA substrate. These models are consistent with results from previous studies and provide both structural and mechanistic insights into the functioning of this unique catalytic RNP complex.
Tsai
Hsin-Yue
HY
Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
Masquida
Benoît
B
Biswas
Roopa
R
Westhof
Eric
E
Gopalan
Venkat
V
D000595:Amino Acid Sequence; D001483:Base Sequence; D020134:Catalytic Domain; D003198:Computer Simulation; D003545:Cysteine / Q000737:chemistry; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000235:genetics; D004492:Edetic Acid; D004722:Endoribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D029968:Escherichia coli Proteins; D019143:Evolution, Molecular; D005296:Ferrous Compounds; D020035:Holoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017665:Hydroxyl Radical / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D021122:Protein Subunits; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D043262:Ribonuclease P
D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D005296:Ferrous Compounds; D020035:Holoenzymes; D021122:Protein Subunits; D012329:RNA, Bacterial; D016337:RNA, Catalytic; C055526:Fe(II)-EDTA; D017665:Hydroxyl Radical; D004492:Edetic Acid; D004722:Endoribonucleases; D043262:Ribonuclease P; C470865:ribonuclease P, E coli; D003545:Cysteine