Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system

Nature Communications
Adrian C D FuchsJörg Martin

Abstract

While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archaeal Rpn11 deubiquitinase from Caldiarchaeum subterraneum, CsRpn11, and its role in the processing of CsUb precursor and ubiquitinated proteins. CsRpn11 activity is affected by the catalytic metal ion type, small molecule inhibitors, sequence characteristics at the cleavage site, and the folding state of CsUb-conjugated proteins. Comparison of CsRpn11 and CsRpn11-CsUb crystal structures reveals a crucial conformational switch in the CsRpn11 Ins-1 site, which positions CsUb for catalysis. The presence of this transition in a primordial soluble Rpn11 thus predates the evolution of eukaryotic Rpn11 immobilized in the proteasomal lid. Complementing phylogenetic studies, which designate CsRpn11 and CsUb as close homologs of the respective eukaryotic proteins, our results provide experimental support for an archaeal origin of protein ubiquitination.

References

Aug 25, 1989·Nucleic Acids Research·A HemsleyD J Galas
Oct 1, 1995·Protein Science : a Publication of the Protein Society·D R HollandB W Matthews
Dec 16, 1998·Trends in Biochemical Sciences·S F Altschul, E V Koonin
Mar 25, 1999·Acta Crystallographica. Section D, Biological Crystallography·G N MurshudovE J Dodson
Nov 28, 2000·Acta Crystallographica. Section D, Biological Crystallography·A Vagin, A Teplyakov
Oct 1, 2003·Biochemistry·Huong J T T TranMark Bycroft
Jan 23, 2004·PLoS Biology·Xavier I AmbroggioRaymond J Deshaies
Jul 31, 2004·Bioinformatics·Tancred Frickey, Andrei Lupas
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
May 28, 2005·Journal of Molecular Biology·Christine M NunnSnezana Djordjevic
Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Kevin Cowtan
Feb 6, 2008·Journal of Proteome Research·Jeffrey JonesLan Huang
Feb 22, 2008·Nucleic Acids Research·Jimin PeiNick V Grishin
Mar 28, 2009·Nature·Mark Hochstrasser
Jun 2, 2009·Current Opinion in Structural Biology·Hitomi Hasegawa, Liisa Holm
Aug 14, 2009·Nature·Kevin J WaldronNigel J Robinson
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Mar 9, 2010·Nature Chemical Biology·Junjun ChenZhihao Zhuang
Mar 9, 2010·Nature Chemical Biology·Champak ChatterjeeTom W Muir
Dec 29, 2011·Frontiers in Bioscience (Landmark Edition)·Alexander Maxwell BurroughsL Aravind
Feb 9, 2012·Journal of Amino Acids·Kayoko M FukasawaJunzo Hirose
Mar 13, 2012·Journal of the American Chemical Society·Franziska MeierMatthew R Pratt
Jun 19, 2013·Nature Structural & Molecular Biology·Mary E MatyskielaAndreas Martin
Jul 13, 2013·Biochimica Et Biophysica Acta·Ziad M Eletr, Keith D Wilkinson
Nov 13, 2013·Physical Chemistry Chemical Physics : PCCP·Benjamin Bouvier
Jan 28, 2014·Nature Structural & Molecular Biology·Evan J WordenAndreas Martin
Feb 12, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ganesh Ramnath PathareWolfgang Baumeister
Jul 6, 2014·Cells·Randy SuryadinataBoris Sarčević
Sep 8, 2015·Nature·Amedee des GeorgesYaser Hashem
Apr 1, 2016·Nature·Simone CavadiniNicolas H Thomä
May 4, 2016·Cellular and Molecular Life Sciences : CMLS·Guinevere L Grice, James A Nathan
Aug 4, 2016·Nature Reviews. Molecular Cell Biology·Lori Buetow, Danny T Huang

❮ Previous
Next ❯

Citations

Dec 1, 2018·Emerging Topics in Life Sciences·Julie A Maupin-Furlow
Dec 15, 2019·Nature Communications·Yusuke SatoShuya Fukai
Mar 11, 2021·Proceedings of the National Academy of Sciences of the United States of America·Adrian C D FuchsAndrei N Lupas
Mar 17, 2021·Proceedings of the National Academy of Sciences of the United States of America·Emma C CarrollSusan Marqusee
Jul 30, 2021·Bioinformatics·Adrian C D FuchsAndrei N Lupas
Sep 10, 2021·Angewandte Chemie·Xingwang ZhangWei Zhang

❮ Previous
Next ❯

Methods Mentioned

BETA
ubiquitination
deubiquitination
circular dichroism
NMR
static light-scattering
co-crystallization
microscale thermophoresis
electrophoresis
gel filtration

Software Mentioned

DALI
DaliLite
REFMAC5
SigmaPlot
PSI
PROMALS3D
ImageJ
Compass DataAnalysis
PyMOL
BLAST

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.

© 2022 Meta ULC. All rights reserved