Structure and RNA binding of the third KH domain of poly(C)-binding protein 1. Nucleic Acids Res

Poly(C)-binding proteins (CPs) are important regu-lators of mRNA stability and translational regulation. They recognize C-rich RNA through their triple KH (hn RNP K homology) domain structures and are thought to carry out their function though direct protection of mRNA sites as well as through interactions with other RNA-binding proteins. We report the crystallograph-ically derived structure of the third domain of aCP1 to 2.1 A ̊ resolution. aCP1-KH3 assumes a classical type I KH domain fold with a triple-stranded b-sheet held against a three-helix cluster in a baabba configura-tion. Its binding affinity to an RNA sequence from the 30-untranslated region (30-UTR) of androgen receptor mRNA was determined using surface plasmon reson-ance, giving a Kd of 4.37 mM, which is indicative of intermediate binding. A model of aCP1-KH3 with poly(C)-RNA was generatedby homology to a recently reported RNA-bound KH domain structure and sug-gests the molecular basis for oligonucleotide binding and poly(C)-RNA specificity.