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Structure of a Shigella effector reveals a new class of ubiquitin ligases

Nature Structural & Molecular Biology volume 15, pages 13021308 (2008) | Download Citation

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Abstract

Bacterial pathogens have evolved effector proteins with ubiquitin E3 ligase activities through structural mimicking. Here we report the crystal structure of the Shigella flexneri type III effector IpaH3, a member of the leucine-rich repeat (LRR)-containing bacterial E3 family. The LRR domain is structurally similar to Yersinia pestis YopM and potentially binds to substrates. The structure of the C-terminal E3 domain differs from the typical RING- and HECT-type E3s. IpaH3 synthesizes a Lys48-linked ubiquitin chain, and the reaction requires noncovalent binding between ubiquitin and a specific E2, UbcH5. Free ubiquitin serves as an acceptor for IpaH3-catalyzed ubiquitin transfer. Cys363 within a conserved CXD motif acts as a nucleophile to catalyze ubiquitin transfer through a transthiolation reaction. The D365N mutant is devoid of E3 activities but turns into a potent ubiquitin-E2 thioesterase. Our analysis establishes a structurally and mechanistically distinct class of ubiquitin ligases found exclusively in pathogenic or symbiotic bacteria.

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Acknowledgements

We thank Y. Yamada and his staff at the KEK Synchrotron Facility (Tsukuba, Japan) and Y. Dong at the Beijing Synchrotron Radiation Facility (BSRF) for assistances with data collection. We thank C. Long and S. Chen for in-house MS analysis and M.W. Silby (Tufts University) for providing the genomic DNA from P. fluorescens PfO-1. We also thank members of the Shao laboratory for helpful discussions and technical assistance. This work was supported by Chinese Ministry of Science and Technology Grant 2005AA210950 and National Basic Research Plan of China grant (2006CB806502) to F.S.

Author information

Author notes

    • Yongqun Zhu
    •  & Hongtao Li

    These authors contributed equally to this work.

Affiliations

  1. National Institute of Biological Sciences, 7# Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.

    • Yongqun Zhu
    • , Hongtao Li
    • , Liyan Hu
    • , Jiayi Wang
    • , Yan Zhou
    • , Zhimin Pang
    • , Liping Liu
    •  & Feng Shao
  2. College of Biotechnology & Food Science, Tianjin University of Commerce, Jinba Road (East entrance), Beichen District, Tianjin, 300134, China.

    • Hongtao Li

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Contributions

Y.Z. performed the crystallography work with assistance from L.H. as well as some of the biochemical assays. H.L. performed most of the biochemical experiments. J.W., Y.Z., Z.P. and L.L. contributed to the generation of reagents. Y.Z., H.L. and F.S. designed the study, interpretated the results and prepared the manuscript.

Corresponding author

Correspondence to Feng Shao.

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https://doi.org/10.1038/nsmb.1517

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