We have used the yeast, Saccharomyces cerevisiae, as a model system to identify a new protein component of the U3 small nucleolar ribonucleoprotein (snoRNP) and to study its role in pre-rRNA processing. Mpp10p, which we have cloned and characterized from humans, mice and yeast, is a 110 kDa protein in yeast. Antibodies to it immunoprecipitate the U3 snoRNA, indicating that it is a U3 snoRNP component. MPP10 is an essential gene. Depletion of Mpp10p by repression of MPP10 expressed from a conditional promoter causes slow growth. Analysis of pre-rRNA processing in the depleted cells indicates that Mpp10p is required for processing at the 3 U3 snoRNA-dependent sites in the pre-rRNA (A0, A1, A2). Truncations of terminal charged domains create Mpp10 proteins that confer slow growth at 30 degrees C and/or at 22 degrees C. Analysis of pre-rRNA processing in these mutants indicates a deficiency in processing at only two of the U3 snoRNA-dependent sites in the pre-rRNA (A1 and A2). Therefore truncated Mpp10 proteins are able to separate the function of the U3 snoRNP into a requirement for it in distinct processing events.