The KH domain of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence

• Published in: RNA (Cambridge) 1998-08, Vol.4 (8), p.998-1006, Article S1355838298980499
• Main Authors: BERGLUND, J. ANDREW, FLEMING, MARGARET L., ROSBASH, MICHAEL
• Format: Article
• Language: English
• Subjects: AIDS/HIV; Amino Acid Sequence; Animals; Base Sequence; Binding Sites; Human immunodeficiency virus 1; Mammals; Models, Molecular; Molecular Sequence Data; Protein Binding; RNA Precursors - metabolism; RNA Splicing; RNA, Messenger - metabolism; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Sequence Homology, Amino Acid; Species Specificity; Yeasts
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1017/S1355838298980499

The yeast and mammalian branchpoint sequence binding proteins (BBP and mBBP/SF1) contain both KH domain and Zn knuckle RNA-binding motifs. The single KH domain of these proteins is sufficient for specific recognition of the pre-mRNA branchpoint sequence (BPS). However, an interaction 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)7 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. Therefore, we propose that all three of these accessory RNA-binding modules bind the phosphate backbone, whereas the KH domain interacts specifically 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 RNA–protein interactions.