Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin

NEMO is essential for activation of the NF-kappa B signaling pathway, which is regulated by ubiquitination of proteins. The C-terminal leucine zipper of NEMO and its adjacent coiled-coil region (CC2-LZ) reportedly bind to linear ubiquitin chains with 1 mu M affinity and to Lys 63-linked chains with 100 mu M affinity. Here we report the crystal structure of the CC2-LZ region of mouse NEMO in complex with Lys 63-linked di-ubiquitin (K63-Ub(2)) at 2.7 angstrom resolution. The ubiquitin-binding region consists of a 130 angstrom-long helix and forms a parallel coiled-coil dimer. The Ile 44-centered hydrophobic patch of ubiquitin is recognized in the middle of the NEMO ubiquitin-binding region. NEMO interacts with each K63-Ub(2) via a single ubiquitin-binding site, consistent with low affinity binding with K63-Ub(2). Structured summary: MINT-7262681: NEMO (uniprotkb:O88522) binds (MI:0407) to Ubiquitin (uniprotkb:P62991) by pull down (MI: 0096) MINT-7262667: Ubiquitin (uniprotkb: P62991) and NEMO (uniprotkb: O88522) bind (MI: 0407) by X-ray crystallography (MI: 0114) (C) 2009 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.