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Articles by David Komander
ZnF-UBP domains regulate deubiquitinase activity by relieving ubiquitin product inhibition
Abstract Most ubiquitin specific protease (USP) deubiquitinases (DUBs) combine non-selective catalytic domains with one or multiple ‘exo’-domains that contribute substrate specificity and localisation, but are generally poorly characterised. Zinc-Finger UBP (ZnF-UBP) domains exist in 12 USP DUBs, yet their function is unclear. We here comprehensively analyse human ZnF-UBP domains, and reveal that 8 of 14 bind ubiquitin (Ub) via an unattached Ub C-terminal GlyGly motif.
Ubiquitination of glycogen and metabolites in cells and tissues
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Abstract Ubiquitin signalling covers a wide range of protein modifications, but its scope may still be underestimated, owing to the ubiquitination of non-proteinaceous substrates, such as sugars, lipids and nucleotides1. The breadth of ubiquitinated non-protein substrates, their abundance and their cellular roles are currently unclear, as current ubiquitinomic and proteomic techniques do not detect non-proteinaceous modifications.
By Marco Jochem, Simon A. Cobbold, Craig Goodman, Catharina Kueng, Anthony Cerra, Laura F. Fielden, Man Lyang Kim, Philipp Schenk, Xiangyi Wang, Simon R. Scutts, Michael Pandos, Lin Tang, Thomas Hermanns, Shane Devine, Martin Brzozowski, Yuri Shibata, Niall Geoghegan, Catriona A. McLean, Bernhard Lechtenberg, Kay H Hofmann, Paul Gregorevic, David Komander
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Nature
Verified
GID/CTLH E3 ligase complex control cell fate programs for sexual development of Plasmodium falciparum
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Abstract Transmission of the malaria parasite Plasmodium falciparum requires the formation of specialised sexual cells called gametocytes. A hallmark of P. falciparum gametocyte development is its long duration, during which the parasite undergoes dramatic cellular remodelling including morphological, physiological and metabolic changes which result in the formation of a transmission ready, stage V gametocyte.
By Danushka Marapana, Sash Lopaticki, Simon A. Cobbold, Niall Geoghegan, Sachin Khurana, Stephen W. Scally, Peter Hickey, Vineet Vaibhav, Sukhdeep K Spall, Jumana Yousef, Laura F Dagley, Christopher D. Goodman, Anton Cozijnsen, Geoffrey I. McFadden, Kelly L. Rogers, Aaron Jex, David Komander, James McCarthy, Christopher J. Tonkin, Matthew Dixon, Alan F. Cowman, Balu Balan, Kitsanapong Reaksudsan, Niva Jayakrishnan
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Nature
Verified
The E3-ome gene-centric compendium reveals the human E3 ligase landscape
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Introduction E3s, the architects of protein ubiquitination, play a pivotal role in shaping the cellular landscape.
By Ngee Kiat Chua, Tania J. Gonzalez-Robles, Cameron J Reddington, Jane Dudley-Fraser, Richard W. Birkinshaw, Jiru Han, Ashleigh Solano, Tomasz Kochańczyk, Joshua Peter, Mark A. Nakasone, Florian Aust, Jacob Munro, Yeh Huei Tong, Julie Iskander, Waruni Abeysekera, Hannah Huckstep, Matthew Ritchie Verified, Ingrid E. Wertz, Sarah G. Hymowitz, Sharad Kumar, Gilbert G. Privé, Alex N. Bullock, Jeffrey J. Babon, Rachel E. Klevit, Sonja Lorenz, Alessio Ciulli, Eric S. Fischer, Nicolas H. Thomä, Radosław Nowak, Brenda A. Schulman, Michael Rape, Katrin Rittinger, Melanie Bahlo, Joel P. Mackay, Peter D. Mace, Christopher D. Lima, Ronald T. Hay, David Komander, Bernhard Lechtenberg, Claudio A.P. Joazeiro, Michele Pagano, Kay H Hofmann, Rebecca Feltham, Alex Garnham, Ron C. Conaway, Julia K. Pagan
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Cell Press
Verified
Ubiquitin-A structural perspective
Keywords ubiquitin ubiquitin chain phospho-ubiquitin linkage specificity post-translational modification non-proteinaceous Get full text access Log in, subscribe or purchase for full access. References 1. Goldstein, G. ∙ Scheid, M. ∙ Hammerling, U. ... Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells Proc. Natl. Acad. Sci. USA. 1975; 72:11-15 2. Varshavsky, A. The early history of the ubiquitin field Protein Sci.
Mutational profiling of SARS-CoV-2 papain-like protease reveals requirements for function, structure, and drug escape - Nature Communications
Abstract Papain-like protease (PLpro) is an attractive drug target for SARS-CoV-2 because it is essential for viral replication, cleaving viral poly-proteins pp1a and pp1ab, and has de-ubiquitylation and de-ISGylation activities, affecting innate immune responses. We employ Deep Mutational Scanning to evaluate the mutational effects on PLpro enzymatic activity and protein stability in mammalian cells.
Just how big is the ubiquitin system? - Nature Structural & Molecular Biology
The modification of proteins with the small protein ubiquitin constitutes a Daedalian system of posttranslational modifications in every eukaryotic cell, which is often referred to as the ubiquitin code1. Here we consider the scale and complexity of the ubiquitin system in light of recent developments.
Deubiquitinases in cancer - Nature Reviews Cancer
Abstract Ubiquitination is an essential regulator of most, if not all, signalling pathways, and defects in cellular signalling are central to cancer initiation, progression and, eventually, metastasis. The attachment of ubiquitin signals by E3 ubiquitin ligases is directly opposed by the action of approximately 100 deubiquitinating enzymes (DUBs) in humans. Together, DUBs and E3 ligases coordinate ubiquitin signalling by providing selectivity for different substrates and/or ubiquitin signals.
Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes - Nature Communications
Abstract Deubiquitinating enzymes are key regulators in the ubiquitin system and an emerging class of drug targets. These proteases disassemble polyubiquitin chains and many deubiquitinases show selectivity for specific polyubiquitin linkages. However, most biochemical insights originate from studies of single diubiquitin linkages in isolation, whereas in cells all linkages coexist.
Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling
Using Affimers as Affinity Matrices for Mass Spectrometry In pull-down applications, the K6 affimer selects its cognate chain type from a mixture of K6, K48, and K63 tetraUb and shows no detectable off-target binding in absence of K6 linkages (Figure 6Figure 6A). Similarly, the K33/K11 affimer quantitatively binds K33 and K11 diUb but fails to pull down K6 diUb (Figure 6Figure 6B).
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