Skip to main content
SpringerLink
Log in

Crystal Structure of the Protein l-Isoaspartyl Methyltransferase from Escherichia coli

  • Original Paper
  • Published:
Cell Biochemistry and Biophysics Aims and scope Submit manuscript

Abstract

Among the known covalent damages that can occur spontaneously to proteins, the formation of isoaspartyl linkages through deamidation of asparagines and isomerization of aspartates may be one of the most rapid forms under conditions of physiological pH and temperature. The protein l-isoaspartyl methyltransferase (PIMT) is thought to recognize l-isoaspartyl residues and repair this kind of damaged proteins. Curiously, there is a potential functional difference between bacterial and mammalian PIMTs. Herein, we present the crystal structure of Escherichia coli PIMT (EcPIMT) at a resolution of 1.8 Å. The enzyme we investigated was able to remain bound to its product S-adenosylhomocysteine (SAH) during crystallization. Analysis indicates that the high affinity of EcPIMT for SAH might lead to the lower activity of the enzyme.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Reissner, K. J., & Aswad, D. W. (2003). Deamidation and isoaspartate formation in proteins: Unwanted alterations or surreptitious signals? Cellular and Molecular Life Sciences, 60(7), 1281–1295.

    Article  CAS  PubMed  Google Scholar 

  2. Perna, A. F., Ingrosso, D., De Santo, N. G., Galletti, P., & Zappia, V. (1995). Mechanism of erythrocyte accumulation of methylation inhibitor S-adenosylhomocysteine in uremia. Kidney International, 47(1), 247–253.

    Article  CAS  PubMed  Google Scholar 

  3. Shirasawa, T., Endoh, R., Zeng, Y. X., Sakamoto, K., & Mori, H. (1995). Protein l-isoaspartyl methyltransferase: Developmentally regulated gene expression and protein localization in the central nervous system of aged rat. Neuroscience Letters, 188(1), 37–40.

    Article  CAS  PubMed  Google Scholar 

  4. Yamamoto, A., Takagi, H., Kitamura, D., Tatsuoka, H., Nakano, H., Kawano, H., et al. (1998). Deficiency in protein l-isoaspartyl methyltransferase results in a fatal progressive epilepsy. Journal of Neuroscience, 18(6), 2063–2074.

    CAS  PubMed  Google Scholar 

  5. Kondo, T., Shirasawa, T., Itoyama, Y., & Mori, H. (1996). Embryonic genes expressed in Alzheimer’s disease brains. Neuroscience Letters, 209(3), 157–160.

    Article  CAS  PubMed  Google Scholar 

  6. David, C. L., Keener, J., & Aswad, D. W. (1999). Isoaspartate in ribosomal protein S11 of Escherichia coli. Journal of Bacteriology, 181(9), 2872–2877.

    CAS  PubMed  Google Scholar 

  7. Kindrachuk, J., Parent, J., Davies, G. F., Dinsmore, M., Attah-Poku, S., & Napper, S. (2003). Overexpression of l-isoaspartate O-methyltransferase in Escherichia coli increases heat shock survival by a mechanism independent of methyltransferase activity. Journal of Biological Chemistry, 278(51), 50880–50886.

    Article  CAS  PubMed  Google Scholar 

  8. Kern, R., Malki, A., Abdallah, J., Liebart, J. C., Dubucs, C., Yu, M. H., et al. (2005). Protein isoaspartate methyltransferase is a multicopy suppressor of protein aggregation in Escherichia coli. Journal of Bacteriology, 187(4), 1377–1383.

    Article  CAS  PubMed  Google Scholar 

  9. Powell, H. R. (1999). The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Crystallographica D: Biological Crystallography, 55(Pt 10), 1690–1695.

    Article  CAS  Google Scholar 

  10. Vagin, A., & Teplyakov, A. (1997). Molrep: An automated program for molecular replacement. Journal of Applied Crystallography, 30, 1022–1025.

    Article  CAS  Google Scholar 

  11. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., et al. (1998). Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallographica D: Biological Crystallography, 54(Pt 5), 905–921.

    Article  CAS  Google Scholar 

  12. Murshudov, G., Vagin, A., & Dodson, E. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica D: Biological Crystallography, 53(Pt 3), 240–255.

    Article  CAS  Google Scholar 

  13. Winn, M. D., Isupov, M. N., & Murshudov, G. N. (2001). Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallographica D: Biological Crystallography, 57(Pt 1), 122–133.

    Article  CAS  Google Scholar 

  14. Emsley, P., & Cowtan, K. (2004). Coot: Model-building tools for molecular graphics. Acta Crystallographica D: Biological Crystallography, 60(Pt 12), 2126–2132.

    Article  Google Scholar 

  15. Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.

    Article  CAS  Google Scholar 

  16. Smith, C. D., Carson, M., Friedman, A. M., Skinner, M. M., Delucas, L., Chantalat, L., et al. (2002). Crystal structure of human l-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-Å resolution and modeling of an isoaspartyl-containing peptide at the active site. Protein Science, 11(3), 625–635.

    Article  CAS  PubMed  Google Scholar 

  17. Tanaka, Y., Tsumoto, K., Yasutake, Y., Umetsu, M., Yao, M., Fukada, H., et al. (2004). How oligomerization contributes to the thermostability of an archaeon protein. Protein l-isoaspartyl-O-methyltransferase from Sulfolobus tokodaii. Journal of Biological Chemistry, 279(31), 32957–32967.

    Article  CAS  PubMed  Google Scholar 

  18. Bennett, E. J., Bjerregaard, J., Knapp, J. E., Chavous, D. A., Friedman, A. M., Royer, W. E., Jr., et al. (2003). Catalytic implications from the Drosophila protein l-isoaspartyl methyltransferase structure and site-directed mutagenesis. Biochemistry, 42(44), 12844–12853.

    Article  CAS  PubMed  Google Scholar 

  19. Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134.

    Article  CAS  PubMed  Google Scholar 

  20. Griffith, S. C., Sawaya, M. R., Boutz, D. R., Thapar, N., Katz, J. E., Clarke, S., et al. (2001). Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its l-isoaspartyl peptide substrate. Journal of Molecular Biology, 313(5), 1103–1116.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Financial support for this project was provided by research grants from the Chinese National Natural Science Foundation (grant nos. 30025012 and 10979039), the Chinese Ministry of Science and Technology (grant nos. 2006CB806500, 2006CB910200, and 2006AA02A318), the Chinese Academy of Sciences (grant no. KSCX2-YW-R-60) and the Chinese Ministry of Education (grant no. 20070358025), Anhui Provincial Natural Science Foundation (grant no. 090413081). We thank Yi Zhu and Xu Cao for their assistance in the plasmid construction.

Author information

Authors and Affiliations

  1. Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, People’s Republic of China

    Pengfei Fang, Xu Li, Jing Wang, Li Xing, Yan Gao, Liwen Niu & Maikun Teng

  2. Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui, 230026, People’s Republic of China

    Pengfei Fang, Xu Li, Jing Wang, Li Xing, Yan Gao, Liwen Niu & Maikun Teng

Authors
  1. Pengfei Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Li Xing
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yan Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Liwen Niu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Maikun Teng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Liwen Niu or Maikun Teng.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fang, P., Li, X., Wang, J. et al. Crystal Structure of the Protein l-Isoaspartyl Methyltransferase from Escherichia coli . Cell Biochem Biophys 58, 163–167 (2010). https://doi.org/10.1007/s12013-010-9103-2

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12013-010-9103-2

Keywords

Search

Navigation