As part of collaborative research carried out by The Netherlands Cancer Institute, Leiden University Medical Centre, Utrecht University, UbiQ and the University of Cologne, Hameed et al. report in Frontiers in Chemistry the synthesis of diubiquitin chains with a fully 15N-labeled distal ubiquitin.

Advanced NMR spectroscopy was used to confirm that diubiquitin proteins adopt different conformations in solution. This structural flexibility is important in binding with ubiquitin-binding domains (UBD) thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interactions is the recognition of K6 linked ubiquitin chains by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using 15N-labeled K6 diubiquitin, the C-terminally extended UBA domain of UBXN1 was shown to confer specificity to K6 diubiquitin while the non-extended version of the domain does not show any linkage preference. Thus, the two distinct conformations of K6 diubiquitin that exist in solution converge into a single conformation upon binding to the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in ubiquitin signaling.

Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1
Dharjath Shahul Hameed1,2, Gabrielle B. A. van Tilburg1,2, Remco Merkx1†, Dennis Flierman1,2, Hans Wienk3†, Farid El Oualid1,4†, Kay Hofmann5, Rolf Boelens3 and Huib Ovaa1,2*
1Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
2Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
3NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
4UbiQ Bio BV, Amsterdam, Netherlands
5Institute for Genetics, University of Cologne, Cologne, Germany

Front. Chem., 22 January 2020 | https://doi.org/10.3389/fchem.2019.00921