NMR Structure of an Archaeal Homologue of Ribonuclease P Protein Rpp29

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Abstract
A protein component of the Archaeoglobus fulgidus RNase P was expressed in Escherichia coli, purified, and structurally characterized using multidimensional NMR methods. The dominant structural feature of this 11 kDa protein is a sheet of six antiparallel β-strands, wrapped around a core of conserved hydrophobic amino acids. Amide proton exchange and 15N relaxation rate data provide evidence that the first 16 residues of the protein, located before the start of the first β-strand, and the last 24 residues, located past the end of the last β-strand, are relatively flexible; this contrasts with the relatively rigid and well-defined structure of the β-sheet. Amino acid sequence comparisons among a diverse set of species indicate that the A. fulgidus protein is homologous to the human RNase P protein Rpp29, yeast RNase P protein Pop4, and a known archaeal RNase P protein from Methanobacter thermoautotrophicus; conserved hydrophobic residues indicate that the homologous protein in each of these species contains a similar β-sheet structure. Conserved surface residues located in the loop connecting strands β2 and β3, the loop connecting strands β4 and β5, and in the flexible N- and C-terminal tails are most likely to have specific interactions with the RNA and other proteins of RNase P. The structural model of an RNase P protein component provided by the present work provides an essential step toward eventually understanding the overall architecture of this complex enzyme and the mechanism by which it performs its functions.