Structural Superimposition

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In eukaryotes, the three RNA polymerases (RNAPs) share a flexible acidic N-terminal tail (NTT) derived from the common subunit RPB6. In human, NTT interacts with the PH domain (PH-D) of the p62 subunit in the general transcription/repair factor TFIIH. Although the respective binding sites are highly conserved in vertebrates, they are poorly conserved in fungi. Here, using NMR spectroscopy, we reveal that in the fission yeast Schizosaccharomyces pombe, NTT interacts with PH-D via a distinct binding mode. In human, NTT adopts a defined structure on the basic surface of PH-D, sequentially forming an acidic string, inserting phenylalanine into a pocket, contributing an acidic beta-strand to a beta-sheet with PH-D, and inserting valine into another pocket. In S. pombe, by contrast, NTT adopts the acidic string and inserts phenylalanine but neither contributes a beta-strand nor inserts valine, suggesting that the former features constitute the core binding elements, whereas the latter provide additional interaction modules. Docking models of S. pombe RNAPs and TFIIH support NTT as a suitable binding platform for TFIIH and suggest that it has a role in transcription elongation and DNA repair. Moreover, substitutions of acidic residues within the NTT affect the stability of Rpb6 in S. pombe cells, and mutant cells expressing Rpb6 variants with selected substitutions exhibit increased sensitivity to methyl methanesulfonate (MMS), which induces DNA damage repaired by nucleotide excision. Collectively, our findings provide structural insight into the conserved function of RPB6 NTT in RNAP-mediated processes.