Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors

Abstract

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 β-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 β-turn with an additional hydrogen bond. Iteration of the peptide structure results in a compact β-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.

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Figure 1: Structure of the CID–CTD complex.
Figure 2: CTD–CID interactions.
Figure 3: CTD β-spiral model.

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Acknowledgements

Part of this work was performed at the Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland. We thank C. Schulze-Briese and the staff of beamline X06SA for help; L. Jacquamet and J. McCarthy for help during data collection at the European Synchrotron Radiation Facility, Grenoble, France; G. Arnold for peptide synthesis; and K. Sträβer and members of the Cramer laboratory for careful reading of the manuscript. P.C. is supported by the Deutsche Forschungsgemeinschaft, the EMBO Young Investigator Programme and the Fonds der Chemischen Industrie. A.M. is supported by an EMBO long-term fellowship.

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Correspondence to Patrick Cramer.

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Supplementary Table 1

Structure determination and refinement statistics. (XLS 18 kb)

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Meinhart, A., Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430, 223–226 (2004). https://doi.org/10.1038/nature02679

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