InterPro domain: IPR038085

This superfamily contains ribonuclease P (Rnp) proteins from eukaryotes and archaea. Rnp is a ubiquitous ribozyme that catalyzes a Mg2+-dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA) [ 1 ]. Archaeal and eukaryote RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins. Eukaryotic and archaeal RNase P RNAs cooperatively function with protein subunits in catalysis [ 2 ].

Eukaryotic nuclear RNase P shares most of its protein components with another essential RNP enzyme, nucleolar RNase MRP [ 3 ]. RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA [ 4 ]. Despite its name, the vast majority of RNase MRP is localized in the nucleolus [ 5 ]. RNase MRP has been shown to cleave primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1) [ 6 ].

Human RNase P is composed of a singular protein Pop1 and three subcomplexes, the Rpp20-Rpp25 heterodimer, Pop5-Rpp14-(Rpp30)2-Rpp40 heteropentamer, and Rpp21-Rpp29-Rpp38 heterotrimer [ 7 ].

In the hyperthermophilic archaeon Pyrococcus horikoshii OT3, RNase P is composed of the RNase P RNA (pRNA) and five proteins (PhoPop5, PhoRpp38, PhoRpp21, PhoRpp29, and PhoRpp30) [ 7 , 8 ].

Proteins in this entry include Rnp2 (also known as Pop5) from archaea and Pop5/Rpp14 from humans. In eukaryotes Pop5 is a subunit of both the Rnp and MRP complexes. Although both Pop5 and Rpp14 have similar protein structure, they share a very limited sequence similarity. Moreover, the C-terminal fragments after the conserved beta sheets in Pop5 and Rpp14 exhibit distinct structural features that mediate interactions with Pop1 and Rpp40, respectively [ 9 ].

The structure of Rnp2 (ribonuclease P protein component 2) has a ferrodoxin-like fold composed of an alpha-beta sandwich with antiparallel beta-sheet and contains an extra C-terminal helix.

1. The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 92, 3809-13
2. Rpp14 and Rpp29, two protein subunits of human ribonuclease P. RNA 5, 153-7
3. Chance and necessity in the evolution of RNase P. RNA 24, 1-5
4. Probing the structure of Saccharomyces cerevisiae RNase MRP. Biochem. Soc. Trans. 33, 479-81
5. Of proteins and RNA: the RNase P/MRP family. RNA 16, 1725-47
6. Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae. RNA 17, 1441-50
7. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem 140, 293-8
8. Structural basis for activation of an archaeal ribonuclease P RNA by protein cofactors. Biosci Biotechnol Biochem 81, 1670-1680