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Structural basis for recognition of diubiquitins by NEMO

Yu-Chih Lo1, Su-Chang Lin, Carla C Rospigliosi

  • 1Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA.

Molecular Cell
|February 3, 2009
PubMed

Insights

NEMO's CC2-LZ region binds diubiquitin chains through complex interfaces. This binding mechanism involves asymmetrical interactions with symmetrical NEMO, revealing key recognition energetics and geometry for NF-kappaB activation.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • NEMO (NF-kappaB Essential Modulator) is the regulatory subunit of IkappaB kinase (IKK).
  • NEMO's CC2-LZ region binds Lys63 (K63)-linked polyubiquitin chains to recruit IKK in NF-kappaB signaling.
  • Tandem diubiquitin binding by NEMO is also observed in vitro.

Purpose of the Study:

  • To elucidate the structural basis of diubiquitin recognition by the NEMO CC2-LZ region.
  • To understand the molecular mechanisms underlying the interaction between NEMO and diubiquitin chains.

Main Methods:

  • X-ray crystallography to determine the structure of the NEMO CC2-LZ region.
  • Mutagenesis studies to investigate the role of specific residues in diubiquitin binding.
  • Nuclear Magnetic Resonance (NMR) experiments to analyze protein-ligand interactions.

Main Results:

  • The crystal structure reveals two dimeric coiled coils (CC2 and LZ) within the NEMO CC2-LZ region.
  • Diubiquitin binding sites are composite surfaces involving both CC2 and LZ regions.
  • Asymmetrical binding of diubiquitin to symmetrical NEMO was observed, with distinct interaction modes for proximal and distal ubiquitins.
  • Specific ubiquitin chains (tandem vs. K63-linked) engage NEMO via unique interfaces, including hydrophobic patches and C-terminal elements.

Conclusions:

  • The study uncovers the detailed energetics and geometry of NEMO-diubiquitin mutual recognition.
  • These findings provide critical insights into the molecular mechanisms of NF-kappaB activation.
  • The complex binding interface highlights the specificity and adaptability of ubiquitin chain recognition by signaling proteins.

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