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SUMO protease SENP1 induces isomerization of the scissile peptide bond

Nature Structural & Molecular Biology volume 13, pages 1069–1077 (2006)Cite this article

Abstract

Small ubiquitin-like modifier (SUMO)-specific protease SENP1 processes SUMO-1, SUMO-2 and SUMO-3 to mature forms and deconjugates them from modified proteins. To establish the proteolytic mechanism, we determined structures of catalytically inactive SENP1 bound to SUMO-1–modified RanGAP1 and to unprocessed SUMO-1. In each case, the scissile peptide bond is kinked at a right angle to the C-terminal tail of SUMO-1 and has the cis configuration of the amide nitrogens. SENP1 preferentially processes SUMO-1 over SUMO-2, but binding thermodynamics of full-length SUMO-1 and SUMO-2 to SENP1 and Km values for processing are very similar. However, kcat values differ by 50-fold. Thus, discrimination between unprocessed SUMO-1 and SUMO-2 by SENP1 is based on a catalytic step rather than substrate binding and is likely to reflect differences in the ability of SENP1 to correctly orientate the scissile bonds in SUMO-1 and SUMO-2.

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Figure 1: Structure of the complex between SENP1 C603A and SUMO-1–modified RanGAP1.
Figure 2: Structure of full-length SUMO-1 bound to SENP1 C603A.
Figure 3: SENP1 C603A induces a conformational change in substrates in solution.
Figure 4: Thermodynamics of substrate and product binding by SENP1 C603A.
Figure 5: Steady-state kinetic analysis of isopeptidase and C-terminal hydrolase activities of SENP1 for SUMO-1 and SUMO-2 substrates.
Figure 6: Proposed mechanism for cleavage of substrates by SENP1.

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Acknowledgements

pHis-TEV-30a was a kind gift from H. Liu, University of St. Andrews. This work was supported by CRUK, AICR and the Wellcome Trust. Structural analysis was carried out in the Scottish Structural Proteomics Facility, which is funded by the Biotechnology Biological Science Research Council and The Scottish Funding Council. J.H.N. is a Biotechnology Biological Science Research Council career development fellow.

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Author notes

  1. Linnan Shen, Michael H Tatham and Changjiang Dong: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre for Interdisciplinary Research, School of Life Science, University of Dundee, DD1 5EH, UK

    Linnan Shen, Michael H Tatham, Anna Zagórska & Ronald T Hay

  2. Centre for Biomolecular Sciences, The University of St Andrews, KY16 9ST, UK

    Changjiang Dong & James H Naismith

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  1. Linnan Shen
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Correspondence to James H Naismith or Ronald T Hay.

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Supplementary information

Supplementary Fig. 1

Final 2Fo – Fc density at scissile bonds. (PDF 282 kb)

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Shen, L., Tatham, M., Dong, C. et al. SUMO protease SENP1 induces isomerization of the scissile peptide bond. Nat Struct Mol Biol 13, 1069–1077 (2006). https://doi.org/10.1038/nsmb1172

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