K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin

Molecular Cell
Yosua Adi KristariyantoYogesh Kulathu

Abstract

Polyubiquitin chains regulate diverse cellular processes through the ability of ubiquitin to form chains of eight different linkage types. Although detected in yeast and mammals, little is known about K29-linked polyubiquitin. Here we report the generation of K29 chains in vitro using a ubiquitin chain-editing complex consisting of the HECT E3 ligase UBE3C and the deubiquitinase vOTU. We determined the crystal structure of K29-linked diubiquitin, which adopts an extended conformation with the hydrophobic patches on both ubiquitin moieties exposed and available for binding. Indeed, the crystal structure of the NZF1 domain of TRABID in complex with K29 chains reveals a binding mode that involves the hydrophobic patch on only one of the ubiquitin moieties and exploits the flexibility of K29 chains to achieve linkage selective binding. Further, we establish methods to study K29-linked polyubiquitin and find that K29 linkages exist in cells within mixed or branched chains containing other linkages.

References

Jul 21, 1995·The Journal of Biological Chemistry·E S JohnsonA Varshavsky
Mar 1, 1995·Molecular and Cellular Biology·J SpenceD Finley
Mar 30, 2001·The Journal of Biological Chemistry·J You, C M Pickart
Jul 23, 2003·Nature Biotechnology·Junmin PengSteven P Gygi
Mar 19, 2004·The EMBO Journal·Steven L AlamWesley I Sundquist
Sep 9, 2005·The EMBO Journal·Kaisa Haglund, Ivan Dikic
Oct 13, 2006·The Biochemical Journal·James H HurleyGali Prag
Jul 21, 2009·Cell·Mathew E SowaJ Wade Harper
Aug 12, 2009·Journal of Molecular Biology·Ajit B DattaCynthia Wolberger
Oct 24, 2009·Nature Reviews. Molecular Cell Biology·Yihong Ye, Michael Rape
Nov 26, 2009·Nature Structural & Molecular Biology·Yogesh KulathuDavid Komander
Dec 2, 2010·Molecular Biology of the Cell·Avital Hay-KorenRina Rosin-Arbesfeld
Feb 1, 2011·The Journal of Biological Chemistry·Eric B DammerJunmin Peng
Mar 24, 2011·Molecular & Cellular Proteomics : MCP·Inbal ZivOded Kleifeld
May 5, 2011·Nature Structural & Molecular Biology·Christian Behrends, J Wade Harper
Dec 6, 2011·Proceedings of the National Academy of Sciences of the United States of America·Yusuke SatoShuya Fukai
Jan 28, 2012·Acta Crystallographica. Section D, Biological Crystallography·Ahmed RohaimSoichi Wakatsuki
Apr 10, 2012·Annual Review of Biochemistry·Koraljka Husnjak, Ivan Dikic
Apr 25, 2012·Annual Review of Biochemistry·David Komander, Michael Rape
Jul 24, 2012·Nature Reviews. Molecular Cell Biology·Yogesh Kulathu, David Komander
Aug 7, 2012·Molecular & Cellular Proteomics : MCP·Amelia C PetersonJoshua J Coon
Apr 9, 2013·Nature Structural & Molecular Biology·Manuela K HospenthalDavid Komander
Aug 30, 2013·Proceedings of the National Academy of Sciences of the United States of America·Christoph H EmmerichPhilip Cohen
Oct 26, 2013·The Journal of Biological Chemistry·Bernard W ChuThomas J Wandless
May 9, 2014·The EMBO Journal·Henrike C BescheAlfred L Goldberg
May 13, 2014·Cell·Hermann-Josef Meyer, Michael Rape
Aug 28, 2014·Nature Communications·Maria Stella RitortoMatthias Trost

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Citations

Feb 24, 2016·Trends in Biochemical Sciences·Caterina AlfanoAnnalisa Pastore
Feb 16, 2016·Structure·Carlos A CastañedaDavid Fushman
Sep 2, 2015·Biochemical and Biophysical Research Communications·Christoph H Emmerich, Philip Cohen
Jun 21, 2015·Current Opinion in Chemical Biology·Grace H Pham, Eric R Strieter
Mar 26, 2016·Cell Research·Kirby N Swatek, David Komander
May 4, 2016·Cellular and Molecular Life Sciences : CMLS·Guinevere L Grice, James A Nathan
May 28, 2016·Nature Cell Biology·Richard Yau, Michael Rape
Jun 9, 2016·Journal of the American Chemical Society·Man PanLei Liu
Jun 18, 2016·Current Opinion in Structural Biology·Gabriëlle Ba van TilburgHuib Ovaa
Oct 17, 2015·Analytical Biochemistry·Serena FaggianoAnnalisa Pastore
Nov 3, 2016·Journal of the American Chemical Society·Shuai GaoLei Liu
Dec 25, 2016·Journal of Biochemistry·Fumiaki Ohtake, Hikaru Tsuchiya
May 10, 2017·Journal of Chemical Theory and Computation·Samuel BowermanJeff Wereszczynski
May 13, 2017·Annual Review of Biochemistry·Tycho E T Mevissen, David Komander
Oct 1, 2015·Physical Chemistry Chemical Physics : PCCP·Carlos A CastañedaDavid Fushman
Feb 26, 2016·Journal of Cell Science·Masato AkutsuAnja Bremm
Aug 16, 2018·Annual Review of Cell and Developmental Biology·Eugene OhMichael Rape
Jan 14, 2017·EMBO Reports·Yosua Adi KristariyantoYogesh Kulathu
Sep 25, 2017·Biochemical Society Transactions·Rachel E HeapMatthias Trost
Dec 10, 2019·Cell Biology International·Akshay Sharma, Arun K Trivedi
May 27, 2016·Biomolecular Concepts·Daichi Morimoto, Masahiro Shirakawa
Feb 11, 2016·Biochemical Society Transactions·Viduth K Chaugule, Helen Walden
Dec 4, 2016·Biochemical Society Transactions·Paul R Elliott
Nov 12, 2018·Parasitology Research·Pu WangXichen Zhang
Feb 11, 2020·Frontiers in Cell and Developmental Biology·Mariska van Huizen, Marjolein Kikkert
May 22, 2016·The Biochemical Journal·Mathew Stanley, Satpal Virdee
Jul 22, 2018·Advanced Science·Qian QuHong-Gang Hu
Jan 31, 2020·Frontiers in Chemistry·Gunnar Dittmar, Konstanze F Winklhofer
Jun 14, 2020·Signal Transduction and Targeted Therapy·Ling ChenYongguang Tao
Feb 11, 2020·Frontiers in Chemistry·Dharjath Shahul HameedHuib Ovaa
Jun 27, 2020·Pharmaceuticals·Hikaru TsuchiyaYasushi Saeki
Jun 7, 2018·Science Signaling·Pengda LiuWenyi Wei

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Methods Mentioned

BETA
pulls down
pull-down
isothermal titration calorimetry
pull down
pull-downs

Software Mentioned

pRM
TRABID

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