DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA


Telomeres, specialized protein–DNA complexes that cap the ends of linear chromosomes, are essential for protecting chromosomes from degradation and end-to-end fusions1,2. The Pot1 (protection of telomeres 1) protein is a widely distributed eukaryotic end-capping protein, having been identified in fission yeast, microsporidia, plants and animals3,4. Schizosaccharomyces pombe Pot1p is essential for telomere maintenance3, and human POT1 has been implicated in telomerase regulation5,6. Pot1 binds telomeric single-stranded DNA (ssDNA) with exceptionally high sequence specificity7, the molecular basis of which has been unknown. Here we describe the 1.9-Å-resolution crystal structure of the amino-terminal DNA-binding domain of S. pombe Pot1p complexed with ssDNA. The protein adopts an oligonucleotide/oligosaccharide-binding (OB) fold8 with two loops that protrude to form a clamp for ssDNA binding. The structure explains the sequence specificity of binding: in the context of the Pot1 protein, DNA self-recognition involving base-stacking and unusual G–T base pairs compacts the DNA. Any sequence change disrupts the ability of the DNA to form this structure, preventing it from contacting the array of protein hydrogen-bonding groups. The structure also explains how Pot1p avoids binding the vast excess of RNA in the nucleus.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Structure of the Pot1pN–ssDNA complex.
Figure 2: Protein–ssDNA and ssDNA–ssDNA interactions in the Pot1pN–GGTTAC complex.
Figure 3: Mutational analysis of residues important for Pot1pN–ssDNA interaction.
Figure 4: The same OB-fold structure adapted for sequence-specific binding.


  1. 1

    Cervantes, R. B. & Lundblad, V. Mechanisms of chromosome-end protection. Curr. Opin. Cell Biol. 14, 351–356 (2002)

    CAS  Article  Google Scholar 

  2. 2

    de Lange, T. Protection of mammalian telomeres. Oncogene 21, 532–540 (2002)

    CAS  Article  Google Scholar 

  3. 3

    Baumann, P. & Cech, T. R. Pot1, the putative telomere end-binding protein in fission yeast and humans. Science 292, 1171–1175 (2001)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Baumann, P., Podell, E. & Cech, T. R. Human Pot1 (protection of telomeres) protein: cytolocalization, gene structure, and alternative splicing. Mol. Cell. Biol. 22, 8079–8087 (2002)

    CAS  Article  Google Scholar 

  5. 5

    Colgin, L. M., Baran, K., Baumann, P., Cech, T. R. & Reddel, R. R. Human POT1 is a positive regulator of telomere length. Curr. Biol. 13, 942–946 (2003)

    CAS  Article  Google Scholar 

  6. 6

    Loayza, D. & de Lange, T. POT1 as a terminal transducer of TRF1 telomere length control. Nature 424, 1013–1018 (2003)

    ADS  Article  Google Scholar 

  7. 7

    Lei, M., Baumann, P. & Cech, T. R. Cooperative binding of single-stranded telomeric DNA by the Pot1 protein of Schizosaccharomyces pombe. Biochemistry 41, 14560–14568 (2002)

    CAS  Article  Google Scholar 

  8. 8

    Murzin, A. G. OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12, 861–867 (1993)

    CAS  Article  Google Scholar 

  9. 9

    Bryan, T. M. & Cech, T. R. Telomerase and the maintenance of chromosome ends. Curr. Opin. Cell Biol. 11, 318–324 (1999)

    CAS  Article  Google Scholar 

  10. 10

    Gray, J. T., Celander, D. W., Price, C. M. & Cech, T. R. Cloning and expression of genes for the Oxytricha telomere-binding protein: specific subunit interactions in the telomeric complex. Cell 67, 807–814 (1991)

    CAS  Article  Google Scholar 

  11. 11

    Horvath, M. P., Schweiker, V. L., Bevilacqua, J. M., Ruggles, J. A. & Schultz, S. C. Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell 95, 963–974 (1998)

    CAS  Article  Google Scholar 

  12. 12

    Mitton-Fry, R. M., Anderson, E. M., Hughes, T. R., Lundblad, V. & Wuttke, D. S. Conserved structure for single-stranded telomeric DNA recognition. Science 296, 145–147 (2002)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Chandra, A., Hughes, T. R., Nugent, C. I. & Lundblad, V. Cdc13 both positively and negatively regulates telomere replication. Genes Dev. 15, 404–414 (2001)

    CAS  Article  Google Scholar 

  14. 14

    Taggart, A. K., Teng, S. C. & Zakian, V. A. Est1p as a cell cycle-regulated activator of telomere-bound telomerase. Science 297, 1023–1026 (2002)

    ADS  CAS  Article  Google Scholar 

  15. 15

    Theobald, D. L., Mitton-Fry, R. M. & Wuttke, D. S. Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 32, 115–133 (2003)

    CAS  Article  Google Scholar 

  16. 16

    Bochkarev, A., Pfuetzner, R. A., Edwards, A. M. & Frappier, L. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385, 176–181 (1997)

    ADS  CAS  Article  Google Scholar 

  17. 17

    Raghunathan, S., Kozlov, A. G., Lohman, T. M. & Waksman, G. Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nature Struct. Biol. 7, 648–652 (2000)

    CAS  Article  Google Scholar 

  18. 18

    Bastin-Shanower, S. A. & Brill, S. J. Functional analysis of the four DNA binding domains of replication protein A. The role of RPA2 in ssDNA binding. J. Biol. Chem. 276, 36446–36453 (2001)

    CAS  Article  Google Scholar 

  19. 19

    Bochkareva, E., Korolev, S., Lees-Miller, S. P. & Bochkarev, A. Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J. 21, 1855–1863 (2002)

    CAS  Article  Google Scholar 

  20. 20

    Hollis, T., Stattel, J. M., Walther, D. S., Richardson, C. C. & Ellenberger, T. Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7. Proc. Natl Acad. Sci. USA 98, 9557–9562 (2001)

    ADS  CAS  Article  Google Scholar 

  21. 21

    Classen, S., Lyons, D., Cech, T. R. & Schultz, S. C. Sequence-specific and 3′-end selective single-stranded DNA binding by Oxytricha nova telomere end binding protein (OnTEBP) α subunit. Biochemistry 42, 9269–9277 (2003)

    CAS  Article  Google Scholar 

  22. 22

    Peersen, O. B., Ruggles, J. A. & Schultz, S. C. Dimeric structure of the Oxytricha nova telomere end-binding protein α-subunit bound to ssDNA. Nature Struct. Biol. 9, 182–187 (2002)

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Classen, S., Ruggles, J. A. & Schultz, S. C. Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein α subunit both uncomplexed and complexed with telomeric ssDNA. J. Mol. Biol. 314, 1113–1125 (2001)

    CAS  Article  Google Scholar 

  24. 24

    Arcus, V. OB-fold domains: a snapshot of the evolution of sequence, structure and function. Curr. Opin. Struct. Biol. 12, 794–801 (2002)

    CAS  Article  Google Scholar 

  25. 25

    Otwinowski, Z. in Proceedings of the CCP4 Study Weekend (eds Sawyer, L., Isaacs, N. & Burley, S.) 56–62 (SERC Daresbury Laboratory, Daresbury, UK, 1993)

    Google Scholar 

  26. 26

    Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    CAS  Article  Google Scholar 

  27. 27

    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 methods. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  28. 28

    Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallogr. 24, 945–950 (1991)

    CAS  Article  Google Scholar 

  29. 29

    Merritt, E. A. & Murphy, M. E. P. Raster 3D version 2.0, a program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869–873 (1994)

    CAS  Article  Google Scholar 

  30. 30

    Nicholls, A. & Honig, B. A rapid finite difference algorithm, utilizing successive overrelaxation to solve Poisson Boltzmann equation. J. Comput. Chem. 270, 26184–26191 (1991)

    Google Scholar 

Download references


We thank F. Guo, L. Chen and D. Theobald for insightful discussions, and G. Meigs and K. Henderson from ALS beamlines 8.2.1 and 8.2.2 for help in data collection. P.B. thanks W. Nudson and J. Bunch for technical assistance. This work was supported by the National Institutes of Health (T.R.C.) and by the Stowers Institute for Medical Research (P.B.). M.L. is a research fellow of the Helen Hay Whitney Foundation.

Author information



Corresponding author

Correspondence to Thomas R. Cech.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lei, M., Podell, E., Baumann, P. et al. DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA. Nature 426, 198–203 (2003). https://doi.org/10.1038/nature02092

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing