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Comparative Study
. 1998 Aug;4(8):998-1006.
doi: 10.1017/s1355838298980499.

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

J A Berglund  1 , M L Fleming, M Rosbash
Affiliations
Comparative Study

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

J A Berglund et al. RNA. 1998 Aug.

Abstract

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.

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