Structural characterization of the ribonuclease P protein aRpp29 from the hyperthermophilic sulfate-reducing Archaeon Archaeoglobus fulgidus

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Sidote, David Joseph

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The process of tRNA maturation requires extensive posttranscriptional modification. These modifications include 5’ leader removal, 3’ CCA addition, intron splicing, and extensive base modification. The enzyme responsible for the removal of the 5’ leader is known as Ribonuclease P (RNase P). This ribonucleoprotein complex is present in all cells and cellular compartments that perform translation. In this dissertation, the archaeal Ribonuclease P protein aRpp29 from Archaeoglobus fulgidus was structurally characterized using nuclear magnetic resonance (NMR) and X-ray crystallography techniques. The structure of aRpp29 consists of an amino terminal α-helix followed by a six-stranded, anti-parallel β-sheet and then an α-helix at the carboxy terminus. The three dimensional structure forms a semi-closed barrel, wrapped around a well-conserved hydrophobic core. The α-helices align in an anti-parallel orientation, capping the open end of the structure. There are well-conserved charged residues that may present a surface for interactions with either the RNase P RNA or the substrate tRNA. An interesting feature of this structure is an internal salt bridge formed by a triad of conserved residues. This feature may confer the unusual stability observed over a wide range of pH and temperatures. The investigation of the structure of aRpp29 using NMR revealed distinct differences when compared to the structure solved using X-ray crystallography. The solution structure forms the same six stranded anti-parallel β-sheet but lacks stable amino and carboxy terminal helices, indicating that ~40% of the protein is in an equilibrium between a folded and unfolded state. This finding was further investigated by measuring circular dichroism and amide proton exchange rates. The structure of aRpp29 reveals that it is a variant of the Sm-fold (or likeSM) family of proteins. These proteins are involved in a variety of processes involving RNA, including splicing and transcriptional regulation. Sm proteins and their homologs form heptameric rings in solution, although untracentrifugation studies show that aRpp29 forms a monomer in solution. The structural studies of archaeal Ribonuclease P protein Rpp29 presented in this dissertation provide an essential step toward understanding the overall architecture of ribonuclease P.



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