A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel

Feng, Peiqiang; Wu, Xudong; Erramilli, Satchal K.; Paulo, Joao A.; Knejski, Pawel; Gygi, Steven P.; Kossiakoff, Anthony A.; Rapoport, Tom A.

doi:10.1038/s41586-022-04903-x

A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel

Journal Article · 01 June 2022 · Nature

DOI:https://doi.org/10.1038/s41586-022-04903-x· OSTI ID:1878394

Feng, Peiqiang; Wu, Xudong; Erramilli, Satchal K.; Paulo, Joao A.; Knejski, Pawel; Gygi, Steven P.; Kossiakoff, Anthony A.; Rapoport, Tom A.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIGMS; NIH

OSTI ID:: 1878394

Journal Information:: Nature, Journal Name: Nature Vol. 607

Country of Publication:: United States

Language:: ENGLISH

References (60)

Protein transport into peroxisomes: Knowns and unknowns Francisco, Tânia; Rodrigues, Tony A.; Dias, Ana F. BioEssays, Vol. 39, Issue 10 https://doi.org/10.1002/bies.201700047	journal	August 2017
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
The peroxisomal importomer constitutes a large and highly dynamic pore Meinecke, Michael; Cizmowski, Christian; Schliebs, Wolfgang Nature Cell Biology, Vol. 12, Issue 3 https://doi.org/10.1038/ncb2027	journal	February 2010
The rat liver peroxisomal membrane forms a permeability barrier for cofactors but not for small metabolites in vitro Antonenkov, V. D. Journal of Cell Science, Vol. 117, Issue 23 https://doi.org/10.1242/jcs.01485	journal	November 2004
Structure of the post-translational protein translocation machinery of the ER membrane Wu, Xudong; Cabanos, Cerrone; Rapoport, Tom A. Nature, Vol. 566, Issue 7742 https://doi.org/10.1038/s41586-018-0856-x	journal	December 2018
Pex10p functions as an E3 ligase for the Ubc4p-dependent ubiquitination of Pex5p Williams, Chris; van den Berg, Marlene; Geers, Erica Biochemical and Biophysical Research Communications, Vol. 374, Issue 4 https://doi.org/10.1016/j.bbrc.2008.07.054	journal	October 2008
Crystal structure of a substrate-engaged SecY protein-translocation channel Li, Long; Park, Eunyong; Ling, JingJing Nature, Vol. 531, Issue 7594 https://doi.org/10.1038/nature17163	journal	March 2016
Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis Plechanovová, Anna; Jaffray, Ellis G.; Tatham, Michael H. Nature, Vol. 489, Issue 7414 https://doi.org/10.1038/nature11376	journal	July 2012
Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways DeLoache, William C.; Russ, Zachary N.; Dueber, John E. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11152	journal	March 2016
Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder Ebberink, Merel S.; Mooijer, Petra A. W.; Gootjes, Jeannette Human Mutation, Vol. 32, Issue 1 https://doi.org/10.1002/humu.21388	journal	December 2010
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
Addressing preferred specimen orientation in single-particle cryo-EM through tilting Tan, Yong Zi; Baldwin, Philip R.; Davis, Joseph H. Nature Methods, Vol. 14, Issue 8 https://doi.org/10.1038/nmeth.4347	journal	July 2017
Insights into the Role of the Peroxisomal Ubiquitination Machinery in Pex13p Degradation in the Yeast Hansenula polymorpha Chen, Xin; Devarajan, Srishti; Danda, Natasha Journal of Molecular Biology, Vol. 430, Issue 11 https://doi.org/10.1016/j.jmb.2018.03.033	journal	May 2018
The RING-type ubiquitin ligases Pex2p, Pex10p and Pex12p form a heteromeric complex that displays enhanced activity in an ubiquitin conjugating enzyme-selective manner: The RING-type ubiquitin ligases El Magraoui, Fouzi; Bäumer, Bastian E.; Platta, Harald W. FEBS Journal, Vol. 279, Issue 11 https://doi.org/10.1111/j.1742-4658.2012.08591.x	journal	May 2012
Distinct Modes of Ubiquitination of Peroxisome-targeting Signal Type 1 (PTS1) Receptor Pex5p Regulate PTS1 Protein Import Okumoto, Kanji; Noda, Hiromi; Fujiki, Yukio Journal of Biological Chemistry, Vol. 289, Issue 20 https://doi.org/10.1074/jbc.M113.527937	journal	March 2014
Quantifying the local resolution of cryo-EM density maps Kucukelbir, Alp; Sigworth, Fred J.; Tagare, Hemant D. Nature Methods, Vol. 11, Issue 1 https://doi.org/10.1038/nmeth.2727	journal	November 2013
Structure of the Sec61 channel opened by a signal sequence Voorhees, R. M.; Hegde, R. S. Science, Vol. 351, Issue 6268 https://doi.org/10.1126/science.aad4992	journal	December 2015
Template-based protein structure modeling using the RaptorX web server Källberg, Morten; Wang, Haipeng; Wang, Sheng Nature Protocols, Vol. 7, Issue 8 https://doi.org/10.1038/nprot.2012.085	journal	July 2012
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data Casañal, Ana; Lohkamp, Bernhard; Emsley, Paul Protein Science, Vol. 29, Issue 4 https://doi.org/10.1002/pro.3791	journal	March 2020
Mechanistic insights into ER-associated protein degradation Wu, Xudong; Rapoport, Tom A. Current Opinion in Cell Biology, Vol. 53 https://doi.org/10.1016/j.ceb.2018.04.004	journal	August 2018
X-ray structure of a protein-conducting channel Berg, Bert van den; Clemons, William M.; Collinson, Ian Nature, Vol. 427, Issue 6969 https://doi.org/10.1038/nature02218	journal	December 2003
Current Advances in Protein Import into Peroxisomes Walter, Thomas; Erdmann, Ralf The Protein Journal, Vol. 38, Issue 3 https://doi.org/10.1007/s10930-019-09835-6	journal	May 2019
Peroxisome biogenesis, membrane contact sites, and quality control Farré, Jean‐Claude; Mahalingam, Shanmuga S.; Proietto, Marco EMBO reports, Vol. 20, Issue 1 https://doi.org/10.15252/embr.201846864	journal	November 2018
Peroxisomal protein import and ERAD: variations on a common theme Schliebs, Wolfgang; Girzalsky, Wolfgang; Erdmann, Ralf Nature Reviews Molecular Cell Biology, Vol. 11, Issue 12 https://doi.org/10.1038/nrm3008	journal	November 2010
Generating Conformation and Complex-Specific Synthetic Antibodies Paduch, Marcin; Kossiakoff, Anthony A. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-6857-2_6	book	January 2017
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
RING Domain E3 Ubiquitin Ligases Deshaies, Raymond J.; Joazeiro, Claudio A. P. Annual Review of Biochemistry, Vol. 78, Issue 1 https://doi.org/10.1146/annurev.biochem.78.101807.093809	journal	June 2009
Pex2 and Pex12 Function as Protein-Ubiquitin Ligases in Peroxisomal Protein Import Platta, H. W.; El Magraoui, F.; Baumer, B. E. Molecular and Cellular Biology, Vol. 29, Issue 20 https://doi.org/10.1128/MCB.00388-09	journal	August 2009
Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs Dominik, Pawel K.; Borowska, Marta T.; Dalmas, Olivier Structure, Vol. 24, Issue 2 https://doi.org/10.1016/j.str.2015.11.014	journal	February 2016
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
New tools for automated high-resolution cryo-EM structure determination in RELION-3 Zivanov, Jasenko; Nakane, Takanori; Forsberg, Björn O. eLife, Vol. 7 https://doi.org/10.7554/eLife.42166	journal	November 2018
Efficient anisotropic refinement of macromolecular structures using FFT Murshudov, Garib N.; Vagin, Alexei A.; Lebedev, Andrey Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 1 https://doi.org/10.1107/S090744499801405X	journal	January 1999
Structure of an E3:E2∼Ub Complex Reveals an Allosteric Mechanism Shared among RING/U-box Ligases Pruneda, Jonathan N.; Littlefield, Peter J.; Soss, Sarah E. Molecular Cell, Vol. 47, Issue 6 https://doi.org/10.1016/j.molcel.2012.07.001	journal	September 2012
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex Wu, Xudong; Siggel, Marc; Ovchinnikov, Sergey Science, Vol. 368, Issue 6489 https://doi.org/10.1126/science.aaz2449	journal	April 2020
BIRC7–E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer Dou, Hao; Buetow, Lori; Sibbet, Gary J. Nature Structural & Molecular Biology, Vol. 19, Issue 9 https://doi.org/10.1038/nsmb.2379	journal	August 2012
A Facile Method for High-throughput Co-expression of Protein Pairs Alexandrov, Andrei; Vignali, Marissa; LaCount, Douglas J. Molecular & Cellular Proteomics, Vol. 3, Issue 9 https://doi.org/10.1074/mcp.T400008-MCP200	journal	July 2004
A Conserved Cysteine Is Essential for Pex4p-dependent Ubiquitination of the Peroxisomal Import Receptor Pex5p Williams, Chris; van den Berg, Marlene; Sprenger, Richard R. Journal of Biological Chemistry, Vol. 282, Issue 31 https://doi.org/10.1074/jbc.M702038200	journal	June 2007
A Conserved Cysteine Residue of Pichia pastoris Pex20p Is Essential for Its Recycling from the Peroxisome to the Cytosol Léon, Sébastien; Subramani, Suresh Journal of Biological Chemistry, Vol. 282, Issue 10 https://doi.org/10.1074/jbc.M611627200	journal	March 2007
High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method Gietz, R. Daniel; Schiestl, Robert H. Nature Protocols, Vol. 2, Issue 1 https://doi.org/10.1038/nprot.2007.13	journal	January 2007
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Ubiquitination of the peroxisomal import receptor Pex5p is required for its recycling Platta, Harald W.; Magraoui, Fouzi El; Schlee, Daniel Journal of Cell Biology, Vol. 177, Issue 2 https://doi.org/10.1083/jcb.200611012	journal	April 2007
The Human Peroxisomal Targeting Signal Receptor, Pex5p, Is Translocated into the Peroxisomal Matrix and Recycled to the Cytosol Dammai, Vincent; Subramani, Suresh Cell, Vol. 105, Issue 2 https://doi.org/10.1016/S0092-8674(01)00310-5	journal	April 2001
The exportomer: the peroxisomal receptor export machinery Platta, Harald W.; Hagen, Stefanie; Erdmann, Ralf Cellular and Molecular Life Sciences, Vol. 70, Issue 8 https://doi.org/10.1007/s00018-012-1136-9	journal	September 2012
Pex18p Is Constitutively Degraded during Peroxisome Biogenesis Purdue, P. Edward; Lazarow, Paul B. Journal of Biological Chemistry, Vol. 276, Issue 50 https://doi.org/10.1074/jbc.M106823200	journal	December 2001
Members of the E2D (UbcH5) Family Mediate the Ubiquitination of the Conserved Cysteine of Pex5p, the Peroxisomal Import Receptor Grou, Cláudia P.; Carvalho, Andreia F.; Pinto, Manuel P. Journal of Biological Chemistry, Vol. 283, Issue 21 https://doi.org/10.1074/jbc.M800402200	journal	May 2008
Recent insights into peroxisome biogenesis and associated diseases Fujiki, Yukio; Abe, Yuichi; Imoto, Yuuta Journal of Cell Science, Vol. 133, Issue 9 https://doi.org/10.1242/jcs.236943	journal	May 2020
The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading Gardner, Brooke M.; Castanzo, Dominic T.; Chowdhury, Saikat Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02474-4	journal	January 2018
Peroxisome Biogenesis Disorders Weller, Sabine; Gould, Stephen J.; Valle, David Annual Review of Genomics and Human Genetics, Vol. 4, Issue 1 https://doi.org/10.1146/annurev.genom.4.070802.110424	journal	September 2003
Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins Rizk, Shahir S.; Paduch, Marcin; Heithaus, John H. Nature Structural & Molecular Biology, Vol. 18, Issue 4 https://doi.org/10.1038/nsmb.2002	journal	March 2011
Reconstitution of the tubular endoplasmic reticulum network with purified components Powers, Robert E.; Wang, Songyu; Liu, Tina Y. Nature, Vol. 543, Issue 7644 https://doi.org/10.1038/nature21387	journal	February 2017
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids Ashkenazy, H.; Erez, E.; Martz, E. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq399	journal	May 2010
Dynamics of the peroxisomal import cycle of PpPex20p: Ubiquitin-dependent localization and regulation Léon, Sébastien; Zhang, Lan; McDonald, W. Hayes Journal of Cell Biology, Vol. 172, Issue 1 https://doi.org/10.1083/jcb.200508096	journal	January 2006
Uniqueness of the mechanism of protein import into the peroxisome matrix: Transport of folded, co-factor-bound and oligomeric proteins by shuttling receptors Léon, Sébastien; Goodman, Joel M.; Subramani, Suresh Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1763, Issue 12 https://doi.org/10.1016/j.bbamcr.2006.08.037	journal	December 2006
Insights into ubiquitin-conjugating enzyme/ co-activator interactions from the structure of the Pex4p:Pex22p complex: Crystal structure of the Pex4p:Pex22p complex Williams, Chris; van den Berg, Marlene; Panjikar, Santosh The EMBO Journal, Vol. 31, Issue 2 https://doi.org/10.1038/emboj.2011.411	journal	November 2011
TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples Li, Jiaming; Van Vranken, Jonathan G.; Pontano Vaites, Laura Nature Methods, Vol. 17, Issue 4 https://doi.org/10.1038/s41592-020-0781-4	journal	March 2020
MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C. BMC Bioinformatics, Vol. 5, Issue 1, p. 113 https://doi.org/10.1186/1471-2105-5-113	journal	August 2004
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Structure and drug resistance of the Plasmodium falciparum transporter PfCRT Kim, Jonathan; Tan, Yong Zi; Wicht, Kathryn J. Nature, Vol. 576, Issue 7786 https://doi.org/10.1038/s41586-019-1795-x	journal	November 2019

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