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.
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Hirose, Y. & Manley, J. L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000)
Proudfoot, N. J., Furger, A. & Dye, M. J. Integrating mRNA processing with transcription. Cell 108, 501–512 (2002)
Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8Ångstrom resolution. Science 292, 1863–1876 (2001)
Komarnitsky, P., Cho, E. J. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452–2460 (2000)
Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13, 67–76 (2004)
Ni, Z., Schwartz, B. E., Werner, J., Suarez, J. R. & Lis, J. T. Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol. Cell 13, 55–65 (2004)
Buratowski, S. The CTD code. Nature Struct. Biol. 10, 679–680 (2003)
Yuryev, A. et al. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl Acad. Sci. USA 93, 6975–6980 (1996)
Patturajan, M., Wei, X., Berezney, R. & Corden, J. L. A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II. Mol. Cell. Biol. 18, 2406–2415 (1998)
Steinmetz, E. J., Conrad, N. K., Brow, D. A. & Corden, J. L. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413, 327–331 (2001)
Barilla, D., Lee, B. A. & Proudfoot, N. J. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 98, 445–450 (2001)
Misra, S., Puertollano, R., Kato, Y., Bonifacino, J. S. & Hurley, J. H. Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains. Nature 415, 933–937 (2002)
Conti, E., Uy, M., Leighton, L., Blobel, G. & Kuriyan, J. Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin α. Cell 94, 193–204 (1998)
Sadowski, M., Dichtl, B., Hubner, W. & Keller, W. Independent functions of yeast Pcf11p in pre-mRNA 3′ end processing and in transcription termination. EMBO J. 22, 2167–2177 (2003)
West, M. L. & Corden, J. L. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140, 1223–1233 (1995)
Suzuki, M. SPXX, a frequent sequence motif in gene regulatory proteins. J. Mol. Biol. 207, 61–84 (1989)
Licatalosi, D. D. et al. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell 9, 1101–1111 (2002)
Verdecia, M. A., Bowman, M. E., Lu, K. P., Hunter, T. & Noel, J. P. Structural basis for phosphoserine–proline recognition by group IV WW domains. Nature Struct. Biol. 7, 639–643 (2000)
Fabrega, C., Shen, V., Shuman, S. & Lima, C. D. Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II. Mol. Cell 11, 1549–1561 (2003)
Kumaki, Y., Matsushima, N., Yoshida, H., Nitta, K. & Hikichi, K. Structure of the YSPTSPS repeat containing two SPXX motifs in the CTD of RNA polymerase II: NMR studies of cyclic model peptides reveal that the SPTS turn is more stable than SPSY in water. Biochim. Biophys. Acta. 1548, 81–93 (2001)
Cagas, P. M. & Corden, J. L. Structural studies of a synthetic peptide derived from the carboxyl-terminal domain of RNA polymerase II. Proteins 21, 149–160 (1995)
Meredith, G. D. et al. The C-terminal domain revealed in the structure of RNA polymerase II. J. Mol. Biol. 258, 413–419 (1996)
Zhang, J. & Corden, J. L. Phosphorylation causes a conformational change in the carboxyl-terminal domain of the mouse RNA polymerase II largest subunit. J. Biol. Chem. 266, 2297–2302 (1991)
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)
Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993)
Smith, G. D., Nagar, B., Rini, J. M., Hauptman, H. A. & Blessing, R. H. The use of SnB to determine an anomalous scattering substructure. Acta. Crystallogr. D 54, 799–804 (1998)
Terwilliger, T. C. Automated structure solution, density modification and model building. Acta. Crystallogr. 58, 1937–1940 (2002)
Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta. Crystallogr. A 47, 110–119 (1991)
Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta. Crystallogr. D 54, 905–921 (1998)
Armache, K. J., Kettenberger, H. & Cramer, P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl Acad. Sci. USA 100, 6964–6968 (2003)
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.
The authors declare that they have no competing financial interests.
About this article
Cite this article
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
Current understanding of CREPT and p15RS, carboxy-terminal domain (CTD)-interacting proteins, in human cancers
Tuning of SPR for Colocalized Characterization of Biomolecules Using Nanoparticle-Containing Multilayers
Transcriptome 3′end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma
Nature Communications (2018)
Nature Communications (2018)
The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA
Nature Communications (2017)