THE KH DOMAIN OF THE BRANCHPOINT SEQUENCE BINDING-PROTEIN DETERMINES SPECIFICITY FOR THE PRE-MESSENGER-RNA BRANCHPOINT SEQUENCE

The yeast and mammalian branchpoint sequence binding proteins (BBP and mBBP/SF1) contain both KH domain and Zn knuckle RNA-binding motifs, T he single KH domain of these proteins is sufficient for specific recog nition of the pre-mRNA branchpoint sequence (BPS), However, an interac tion is only apparent if one or more accessory modules are present to increase binding affinity. The Zn knuckles of BBP/mBBP can be replaced by an RNA-binding peptide derived from the HIV-1 nucleocapsid protein or by an arginine-serine (RS)I peptide, without loss of specificity. Only the seven-nucleotide branchpoint sequence and two nucleotides to either side are necessary for RNA binding to the chimeric proteins. Th erefore, we propose that all three of these accessory RNA-binding modu les bind the phosphate backbone, whereas the KH domain interacts speci fically with the bases of the BPS. Proteins and protein complexes with multiple RNA-binding motifs are frequent, suggesting that an intimate collaboration between two or more motifs will be a general theme in R NA-protein interactions.