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Recognition of RNA polymerase II carboxy−terminal domain by 3'−RNA−processing factors


Meinhart,  Anton
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Max Planck Society;

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Meinhart, A., & Cramer, P. (2004). Recognition of RNA polymerase II carboxy−terminal domain by 3'−RNA−processing factors. Nature, 430(6996), 223-226. doi:10.1038/nature02679.

During transcription, RNA polymerase (Pol) II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing by the carboxy−terminal domain (CTD) of Pol II, which consists of up to 52 repeats of the sequence Tyr 1−Ser 2−Pro 3−Thr 4−Ser 5−Pro 6−Ser 7 (refs 1, 2). After phosphorylation, the CTD binds tightly to a conserved CTD−interacting domain (CID) present in the proteins Pcf11 and Nrd1, which are essential and evolutionarily conserved factors for polyadenylation−dependent and −independent 3'−RNA processing, respectively. Here we describe the structure of a Ser 2−phosphorylated CTD peptide bound to the CID domain of Pcf11. The CTD motif Ser 2−Pro 3−Thr 4−Ser 5 forms a beta−turn that binds to a conserved groove in the CID domain. The Ser 2 phosphate group does not make direct contact with the CID domain, but may be recognized indirectly because it stabilizes the beta−turn with an additional hydrogen bond. Iteration of the peptide structure results in a compact beta−spiral model of the CTD. The model suggests that, during the mRNA transcription−processing cycle, compact spiral regions in the CTD are unravelled and regenerated in a phosphorylation−dependent manner