Prp8 contains a conserved RNA recognition motif (RRM). Using a hidden Markov model with the HMMER package (Eddy 1998) against the human NCBI database, only RRM containing proteins were identified. (The model is available as Supplementary Data at http://www.ed.ac.uk/~jeanb/; Supplemental Fig. S1). The alignment between 10 different Prp8 sequences and nine known RRMs from the Interpro database is carried out using ClustalW or T-coffee in combination with Jalview (Thompson et al. 1994; Notredame et al. 2000). The conserved RNP-1 and RNP-2 motifs are boxed and highlighted in bold blue type. A number of mutations are known in yeast Prp8 that suppress brr2–1 and/or U4–cs1 mutations and these are highlighted by bold red underlined text. A unique feature of Prp8’s RRM is the conserved amino acid triplet KDM in the center of the domain. The consensus calculations are derived from 25 different Prp8p sequences from 23 species using ClustalW and the online “consensus” program. A stylized representation of the RRM secondary structure based on the U1A crystal structure is shown between the primary sequences.
