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

Author

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  • Anton Meinhart

    (Gene Center, University of Munich)

  • Patrick Cramer

    (Gene Center, University of Munich)

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.

Suggested Citation

  • Anton Meinhart & Patrick Cramer, 2004. "Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors," Nature, Nature, vol. 430(6996), pages 223-226, July.
    • Handle: RePEc:nat:nature:v:430:y:2004:i:6996:d:10.1038_nature02679
    DOI: 10.1038/nature02679
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    Cited by:

    1. Matthew J Betts & Oliver Wichmann & Mathias Utz & Timon Andre & Evangelia Petsalaki & Pablo Minguez & Luca Parca & Frederick P Roth & Anne-Claude Gavin & Peer Bork & Robert B Russell, 2017. "Systematic identification of phosphorylation-mediated protein interaction switches," PLOS Computational Biology, Public Library of Science, vol. 13(3), pages 1-20, March.
    2. Lisa-Marie Appel & Vedran Franke & Melania Bruno & Irina Grishkovskaya & Aiste Kasiliauskaite & Tanja Kaufmann & Ursula E. Schoeberl & Martin G. Puchinger & Sebastian Kostrhon & Carmen Ebenwaldner & M, 2021. "PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC," Nature Communications, Nature, vol. 12(1), pages 1-24, December.
    3. Lisa-Marie Appel & Vedran Franke & Johannes Benedum & Irina Grishkovskaya & Xué Strobl & Anton Polyansky & Gregor Ammann & Sebastian Platzer & Andrea Neudolt & Anna Wunder & Lena Walch & Stefanie Kais, 2023. "The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    4. David Flores-Solis & Irina P. Lushpinskaia & Anton A. Polyansky & Arya Changiarath & Marc Boehning & Milana Mirkovic & James Walshe & Lisa M. Pietrek & Patrick Cramer & Lukas S. Stelzl & Bojan Zagrovi, 2023. "Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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