All Publications

  • Selective Binding of AIRAPL Tandem UIMs to Lys48-Linked Tri-Ubiquitin Chains. Structure Rahighi, S., Braunstein, I., Ternette, N., Kessler, B., Kawasaki, M., Kato, R., Matsui, T., Weiss, T. M., Stanhill, A., Wakatsuki, S. 2016; 24 (3): 412-422


    Lys48-linked ubiquitin chains act as the main targeting signals for protein degradation by the proteasome. Here we report selective binding of AIRAPL, a protein that associates with the proteasome upon exposure to arsenite, to Lys48-linked tri-ubiquitin chains. AIRAPL comprises two ubiquitin-interacting motifs in tandem (tUIMs) that are linked through a flexible inter-UIM region. In the complex crystal structure UIM1 binds the proximal ubiquitin, whereas UIM2 (the double-sided UIM) binds non-symmetrically to the middle and distal ubiquitin moieties on either side of the helix. Specificity of AIRAPL for Lys48-linked ubiquitin chains is determined by UIM2, and the flexible inter-UIM linker increases avidity by placing the two UIMs in an orientation that facilitates binding of the third ubiquitin to UIM1. Unlike middle and proximal ubiquitins, distal ubiquitin binds UIM2 through a novel surface, which leaves the Ile44 hydrophobic patch accessible for binding to the proteasomal ubiquitin receptors.

    View details for DOI 10.1016/j.str.2015.12.017

    View details for PubMedID 26876100

  • Crystal Structure of a PCP/Sfp Complex Reveals the Structural Basis for Carrier Protein Posttranslational Modification CHEMISTRY & BIOLOGY Tufar, P., Rahighi, S., Kraas, F. I., Kirchner, D. K., Loehr, F., Henrich, E., Koepke, J., Dikic, I., Guentert, P., Marahiel, M. A., Doetsch, V. 2014; 21 (4): 552-562


    Phosphopantetheine transferases represent a class of enzymes found throughout all forms of life. From a structural point of view, they are subdivided into three groups, with transferases from group II being the most widespread. They are required for the posttranslational modification of carrier proteins involved in diverse metabolic pathways. We determined the crystal structure of the group II phosphopantetheine transferase Sfp from Bacillus in complex with a substrate carrier protein in the presence of coenzyme A and magnesium, and observed two protein-protein interaction sites. Mutational analysis showed that only the hydrophobic contacts between the carrier protein's second helix and the C-terminal domain of Sfp are essential for their productive interaction. Comparison with a similar structure of a complex of human proteins suggests that the mode of interaction is highly conserved in all domains of life.

    View details for DOI 10.1016/j.chembiol.2014.02.014

    View details for Web of Science ID 000335431300017

    View details for PubMedID 24704508

  • Mechanism Underlying I kappa B Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex MOLECULAR AND CELLULAR BIOLOGY Fujita, H., Rahighi, S., Akita, M., Kato, R., Sasaki, Y., Wakatsuki, S., Iwai, K. 2014; 34 (7): 1322-1335


    The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex.

    View details for DOI 10.1128/MCB.01538-13

    View details for Web of Science ID 000332696800013

    View details for PubMedID 24469399

  • Selectivity of the ubiquitin-binding modules FEBS LETTERS Rahighi, S., Dikic, I. 2012; 586 (17): 2705-2710


    Ubiquitin-binding modules are constituents of cellular proteins that mediate the effects of ubiquitylation by making transient, non-covalent interactions with ubiquitin molecules. While some ubiquitin-binding modules bind single ubiquitin moieties, others are selective for specific ubiquitin chains of different linkage types and lengths. In recent years, functions of ubiquitin chains that are polymerized through their Lys or N-terminal Met (i.e. linear chains) residues have been linked to a variety of cellular processes. Selectivity of ubiquitin-binding modules for different ubiquitin chain types appears as a key to the distinct regulatory consequences during protein quality control pathways, receptor endocytosis, gene transcription, signaling via the NF-κB pathway, and autophagy.

    View details for DOI 10.1016/j.febslet.2012.04.053

    View details for Web of Science ID 000307295200017

    View details for PubMedID 22569095

  • Conformational flexibility and rotation of the RING domain in activation of cullin-RING ligases NATURE STRUCTURAL & MOLECULAR BIOLOGY Rahighi, S., Dikic, I. 2011; 18 (8): 863-865

    View details for Web of Science ID 000293457200002

    View details for PubMedID 21811311

  • Selective Binding of Linear Ubiquitin Chains to NEMO in NF-kappaB Activation ADVANCES IN TNF FAMILY RESEARCH Ikeda, F., Rahighi, S., Wakatsuki, S., Dikic, I. 2011; 691: 107-114

    View details for DOI 10.1007/978-1-4419-6612-4_11

    View details for Web of Science ID 000291501300013

    View details for PubMedID 21153314

  • Unusual Antibacterial Property of Mesoporous Titania Films: Drastic Improvement by Controlling Surface Area and Crystallinity CHEMISTRY-AN ASIAN JOURNAL Oveisi, H., Rahighi, S., Jiang, X., Nemoto, Y., Beitollahi, A., Wakatsuki, S., Yamauchi, Y. 2010; 5 (9): 1978-1983

    View details for DOI 10.1002/asia.201000351

    View details for Web of Science ID 000281916600006

    View details for PubMedID 20665652

  • Specific Recognition of Linear Ubiquitin Chains by NEMO Is Important for NF-kappa B Activation CELL Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S., Dikic, I. 2009; 136 (6): 1098-1109


    Activation of nuclear factor-kappaB (NF-kappaB), a key mediator of inducible transcription in immunity, requires binding of NF-kappaB essential modulator (NEMO) to ubiquitinated substrates. Here, we report that the UBAN (ubiquitin binding in ABIN and NEMO) motif of NEMO selectively binds linear (head-to-tail) ubiquitin chains. Crystal structures of the UBAN motif revealed a parallel coiled-coil dimer that formed a heterotetrameric complex with two linear diubiquitin molecules. The UBAN dimer contacted all four ubiquitin moieties, and the integrity of each binding site was required for efficient NF-kappaB activation. Binding occurred via a surface on the proximal ubiquitin moiety and the canonical Ile44 surface on the distal one, thereby providing specificity for linear chain recognition. Residues of NEMO involved in binding linear ubiquitin chains are required for NF-kappaB activation by TNF-alpha and other agonists, providing an explanation for the detrimental effect of NEMO mutations in patients suffering from X-linked ectodermal dysplasia and immunodeficiency.

    View details for DOI 10.1016/j.cell.2009.03.007

    View details for Web of Science ID 000264403900015

    View details for PubMedID 19303852