NMR resonance assignments of the NZF domain of mouse HOIL-1L free and bound to linear di-ubiquitin

Abstract

Nuclear factor-κB (NF-κB) activation plays a central role in immunity and inflammation. In the canonical NF-κB activation pathway, linear polyubiquitin chains conjugated by the linear ubiquitin chain assembly complex (LUBAC) are specifically recognized by the Npl4 zinc finger (NZF) domain of heme-oxidized IRP2 ligase-1L (HOIL-1L). Recently, a crystal structure of the NZF domain in complex with linear di-ubiquitin has been reported; however, to understand the recognition mechanism in more detail, it is also necessary to investigate the structure and dynamics of the NZF domain in solution. In this study, we report the 1H, 13C, and 15N backbone and side chain resonance assignments of the NZF domain in the free form as well as the backbone resonance assignments of the NZF domain in the di-ubiquitin-bound form. Based on the assigned chemical shifts, we analyzed the secondary structure propensity, suggesting that the free form of the NZF domain forms secondary structure elements as observed in the di-ubiquitin-bound form. We expect that our data will provide an important basis for characterization of the free NZF domain and elucidation of the detailed recognition mechanism in solution.

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References

  1. Delaglio F, Grzesiek S, Vuister G et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293

    Article  Google Scholar 

  2. Fujita H, Tokunaga A, Shimizu S et al (2018) Cooperative domain formation by homologous motifs in HOIL-1L and SHARPIN plays a crucial role in LUBAC stabilization. Cell Rep 23:1192–1204

    Article  Google Scholar 

  3. Hayden MS, Ghosh S (2004) Signaling to NF-κB. Genes Dev 18:2195–2224

    Article  Google Scholar 

  4. Johnson BA, Blevins RA (1994) NMR view: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614

    Article  Google Scholar 

  5. Karin M, Greten FR (2005) NF-κB: linking inflammation and immunity to cancer development and progression. Nat Rev Immunol 5:749–759

    Article  Google Scholar 

  6. Kirisako T, Kamei K, Murata S et al (2006) A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J 25:4877–4887

    Article  Google Scholar 

  7. Kobayashi N, Iwahara J, Koshiba S et al (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR 39:31–52

    Article  Google Scholar 

  8. Kornhaber GJ, Snyder D, Moseley HNB, Montelione GT (2006) Identification of zinc-ligated cysteine residues based on 13Cα and 13Cβ chemical shift data. J Biomol NMR 34:259–269

    Article  Google Scholar 

  9. Markley JL, Bax A, Arata Y et al (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Biomol NMR 12:1–23

    Article  Google Scholar 

  10. Marsh JA, Singh VK, Jia Z, Forman-Kay JD (2006) Sensitivity of secondary structure propensities to sequence differences between α- and γ-synuclein: implications for fibrillation. Protein Sci 15:2795–2804

    Article  Google Scholar 

  11. Morimoto D, Walinda E, Fukada H et al (2015) The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates. Nat Commun 6:6116

    Article  Google Scholar 

  12. Rahighi S, Ikeda F, Kawasaki M et al (2009) Specific recognition of linear ubiquitin chains by NEMO is important for NF-κB activation. Cell 136:1098–1109

    Article  Google Scholar 

  13. Sato Y, Fujita H, Yoshikawa A et al (2011) Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proc Natl Acad Sci USA 108:20520–20525

    ADS  Article  Google Scholar 

  14. Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34:93–158

    Article  Google Scholar 

  15. Schmidt E, Güntert P (2012) A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 134:12817–12829

    Article  Google Scholar 

  16. Tokunaga F, Sakata SI, Saeki Y et al (2009) Involvement of linear polyubiquitylation of NEMO in NF-κB activation. Nat Cell Biol 11:123–132

    Article  Google Scholar 

  17. Tokunaga F, Nakagawa T, Nakahara M et al (2011) SHARPIN is a component of the NF-κB-activating linear ubiquitin chain assembly complex. Nature 471:633–636

    ADS  Article  Google Scholar 

  18. Vallabhapurapu S, Karin M (2009) Regulation and Function of NF-κB transcription factors in the immune system. Annu Rev Immunol 27:693–733

    Article  Google Scholar 

  19. Yamazaki T, Forman-Kay JD, Kay LE (1993) Two-dimensional NMR experiments for correlating 13Cβ and 1Hδ/ε chemical shifts of aromatic residues in 13C-labeled proteins via scalar couplings. J Am Chem Soc 115:11054–11055

    Article  Google Scholar 

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Acknowledgements

This study was supported by JSPS KAKENHI Grant Number 18K14665 and the Japan Agency for Medical Research and Development (AMED, Grant Number JP16gm0510004).

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Correspondence to Masahiro Shirakawa.

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The authors declare no competing financial interests.

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Ishii, N., Walinda, E., Iwakawa, N. et al. NMR resonance assignments of the NZF domain of mouse HOIL-1L free and bound to linear di-ubiquitin. Biomol NMR Assign 13, 149–153 (2019). https://doi.org/10.1007/s12104-018-09868-5

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Keywords

  • NF-κB
  • LUBAC
  • HOIL-1L
  • Npl4 zinc finger
  • Linear polyubiquitin