Structural basis for the recognition of the S2, S5‐phosphorylated RNA polymerase II CTD by the mRNA anti‐terminator protein hSCAF4.

The C‐terminal domain (CTD) of RNA polymerase II serves as a binding platform for numerous enzymes and transcription factors involved in nascent RNA processing and the transcription cycle. The S2, S5‐phosphorylated CTD is recognized by the transcription factor SCAF4, which functions as a transcription anti‐terminator by preventing early mRNA transcript cleavage and polyadenylation. Here, we measured the binding affinities of differently modified CTD peptides by hSCAF4 and solved the complex structure of the hSCAF4‐CTD‐interaction domain (CID) bound to a S2, S5‐quadra‐phosphorylated CTD peptide. Our results revealed that the S2, S5‐quadra‐phosphorylated CTD peptide adopts a trans conformation and is located in a positively charged binding groove of hSCAF4‐CID. Although hSCAF4‐CID has almost the same binding pattern to the CTD as other CID‐containing proteins, it preferentially binds to the S2, S5‐phosphorylated CTD. Our findings provide insight into the regulatory mechanism of hSCAF4 in transcription termination. [ABSTRACT FROM AUTHOR]