VARIATIONS OF THE C2H2 ZINC-FINGER MOTIF IN THE YEAST GENOME AND CLASSIFICATION OF YEAST ZINC-FINGER PROTEINS

The PROSITE pattern Zinc_Finger_C2H2 was extended to permit the detect ion of all C2H2 zinc fingers and their parent proteins in the recently completed sequence of the yeast genome. Additionally, a new computer program was written that extracts other zinc binding motifs (non C2H2 'fingers'), overlapping with the classical zinc finger pattern, from t he found set of yeast C2H2 fingers. The complete and correct detection of all fingers is a prerequisite for the classification of the yeast zinc finger proteins in functional terms. The detected 53 yeast C2H2 z inc finger proteins do not contain finger clusters with 10 or more rep eats, as is frequently found in higher eukaryotes. Only three proteins contain four or more fingers in a cluster. Moreover, nearly all 27 ye ast proteins with tandem arrays of two or three finger domains can be classified into nine subgroups with high sequence conservation in thei r finger clusters, in particular of their DNA recognition helices. The se results and application of the recently elaborated finger/DNA recog nition rules suggest that the yeast proteins belonging to the same sub group may recognize identical or very similar DNA sites.