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RNase P has mostly been studied in Bacteria. In these organisms, RNase P is composed of two subunits: a large RNA, and a small protein. It is the RNA subunit, not the protein, that is the catalyst - in fact, under somewhat higher than physiological ionic strength in vitro, the RNA by itself (without the protein) can efficiently bind pre-tRNA, cleave off the leader, and release the products, over and over. In other words, the RNA subunit of RNase P is a catalytically-active RNA, an "RNA enzyme" or "ribozyme". It is because of this that the bacterial RNase P RNA has been so extensively studied, perhaps at the expense of other interesting aspects of the enzyme: the protein, regulation of the genes that encode the subunits, and the more complex bacterial and eukaryotic systems, for example.

The small protein subunit acts as an accessory factor; it allows the RNA to function well under physiological conditions, and provides the ability of the holoenzyme to distinguish substrate pre-tRNA from product mature tRNA, thus relieving the holoenzyme from product inhibition. In vivo, the protein is essential.

Good three-dimensional structures of the protein subunit from several species has been determined, but although there are a few three-dimensional structures of the RNA, these all have significant weaknesses or are very incomplete, and there are no holoenzyme structures. The secondary structure of the RNA has been determined to very high resolution by comparative sequence analysis, and a number of tertiary interactions have also been identified (we worked on this before moving to the archaeal system). There are two very nice models for the three-dimensional structure of the RNA based on this information and crosslinking data, and these are in good agreement with each other and with the preliminary structures available so far. The general sites of interaction of the RNA with the substrate and the catalyic center are known, and the probable site of interaction of the protein with the leader of the substrate is also known. However, where the protein binds the RNA, and where on the protein the RNase P RNA binds, are still not well defined.

The secondary structure of the E. coli RNase P RNA in the slide is colorized according to sequence conservation; conservation at each position in the alignment of approximately 300 type A bacterial RNase P RNAs is measured by an entropy coefficient H. At one end of the spectrum, dark blue represents invariant bases, progressing from blue to cyan, green, yellow, orange, read and finally violet with increasing sequence variability.