Structure of the Cdc48 ATPase with Its Ubiquitin-binding Cofactor Ufd1-Npl4

Overview

Journal Nat Struct Mol Biol

Specialties Cell Biology
Molecular Biology

Date 2018 Jul 4

PMID 29967539

Citations 52

Authors

Nicholas O Bodnar

Kelly H Kim

Zhejian Ji

Thomas E Wales

Vladimir Svetlov

Evgeny Nudler

John R Engen

Thomas Walz

Tom A Rapoport

Affiliations

Soon will be listed here.

Abstract

Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn-finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.

Citing Articles

The role of SUMOylation in biomolecular condensate dynamics and protein localization.

Gutierrez-Morton E, Wang Y Cell Insight. 2024; 3(6):100199.

PMID: 39399482 PMC: 11467568. DOI: 10.1016/j.cellin.2024.100199.

Mechanisms and regulation of substrate degradation by the 26S proteasome.

Arkinson C, Dong K, Gee C, Martin A Nat Rev Mol Cell Biol. 2024; 26(2):104-122.

PMID: 39362999 PMC: 11772106. DOI: 10.1038/s41580-024-00778-0.

Chemical Synthesis of Human Proteoforms and Application in Biomedicine.

Ai H, Pan M, Liu L ACS Cent Sci. 2024; 10(8):1442-1459.

PMID: 39220697 PMC: 11363345. DOI: 10.1021/acscentsci.4c00642.

A non-symmetrical p97 conformation initiates a multistep recruitment of Ufd1/Npl4.

Arie M, Matzov D, Karmona R, Szenkier N, Stanhill A, Navon A iScience. 2024; 27(6):110061.

PMID: 38947518 PMC: 11214410. DOI: 10.1016/j.isci.2024.110061.

The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions.

Braxton J, Altobelli C, Tucker M, Tse E, Thwin A, Arkin M Nat Struct Mol Biol. 2023; 30(12):2009-2019.

PMID: 37945741 PMC: 10716044. DOI: 10.1038/s41594-023-01126-0.

References

Rohou A, Grigorieff N . CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015; 192(2):216-21. PMC: 6760662. DOI: 10.1016/j.jsb.2015.08.008. View

DeHoratius C, Silver P . Nuclear transport defects and nuclear envelope alterations are associated with mutation of the Saccharomyces cerevisiae NPL4 gene. Mol Biol Cell. 1996; 7(11):1835-55. PMC: 276030. DOI: 10.1091/mbc.7.11.1835. View

Heo J, Livnat-Levanon N, Taylor E, Jones K, Dephoure N, Ring J . A stress-responsive system for mitochondrial protein degradation. Mol Cell. 2010; 40(3):465-80. PMC: 2998070. DOI: 10.1016/j.molcel.2010.10.021. View

Ohi M, Li Y, Cheng Y, Walz T . Negative Staining and Image Classification - Powerful Tools in Modern Electron Microscopy. Biol Proced Online. 2004; 6:23-34. PMC: 389902. DOI: 10.1251/bpo70. View

Evans P, Murshudov G . How good are my data and what is the resolution?. Acta Crystallogr D Biol Crystallogr. 2013; 69(Pt 7):1204-14. PMC: 3689523. DOI: 10.1107/S0907444913000061. View

Isaacson R, Pye V, Simpson P, Meyer H, Zhang X, Freemont P . Detailed structural insights into the p97-Npl4-Ufd1 interface. J Biol Chem. 2007; 282(29):21361-9. DOI: 10.1074/jbc.M610069200. View

Lee C, Prakash S, Matouschek A . Concurrent translocation of multiple polypeptide chains through the proteasomal degradation channel. J Biol Chem. 2002; 277(38):34760-5. DOI: 10.1074/jbc.M204750200. View

Park S, Isaacson R, Kim H, Silver P, Wagner G . Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Structure. 2005; 13(7):995-1005. DOI: 10.1016/j.str.2005.04.013. View

Terwilliger T, Grosse-Kunstleve R, Afonine P, Moriarty N, Zwart P, Hung L . Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr. 2007; 64(Pt 1):61-9. PMC: 2394820. DOI: 10.1107/S090744490705024X. View

10.

Bodnar N, Rapoport T . Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex. Cell. 2017; 169(4):722-735.e9. PMC: 5751438. DOI: 10.1016/j.cell.2017.04.020. View

11.

McCoy A, Grosse-Kunstleve R, Adams P, Winn M, Storoni L, Read R . Phaser crystallographic software. J Appl Crystallogr. 2009; 40(Pt 4):658-674. PMC: 2483472. DOI: 10.1107/S0021889807021206. View

12.

DeLaBarre B, Christianson J, Kopito R, Brunger A . Central pore residues mediate the p97/VCP activity required for ERAD. Mol Cell. 2006; 22(4):451-62. DOI: 10.1016/j.molcel.2006.03.036. View

13.

Scheres S . RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 2012; 180(3):519-30. PMC: 3690530. DOI: 10.1016/j.jsb.2012.09.006. View

14.

Hanzelmann P, Schindelin H . The Interplay of Cofactor Interactions and Post-translational Modifications in the Regulation of the AAA+ ATPase p97. Front Mol Biosci. 2017; 4:21. PMC: 5389986. DOI: 10.3389/fmolb.2017.00021. View

15.

Punjani A, Rubinstein J, Fleet D, Brubaker M . cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods. 2017; 14(3):290-296. DOI: 10.1038/nmeth.4169. View

16.

Burton R, Siddiqui S, Kim Y, Baker T, Sauer R . Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO J. 2001; 20(12):3092-100. PMC: 150209. DOI: 10.1093/emboj/20.12.3092. View

17.

Tsuchiya H, Ohtake F, Arai N, Kaiho A, Yasuda S, Tanaka K . In Vivo Ubiquitin Linkage-type Analysis Reveals that the Cdc48-Rad23/Dsk2 Axis Contributes to K48-Linked Chain Specificity of the Proteasome. Mol Cell. 2017; 66(4):488-502.e7. DOI: 10.1016/j.molcel.2017.04.024. View

18.

Li X, Zheng S, Agard D, Cheng Y . Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage. J Struct Biol. 2015; 192(2):174-8. PMC: 4633327. DOI: 10.1016/j.jsb.2015.09.003. View

19.

Li X, Mooney P, Zheng S, Booth C, Braunfeld M, Gubbens S . Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods. 2013; 10(6):584-90. PMC: 3684049. DOI: 10.1038/nmeth.2472. View

20.

Zheng S, Palovcak E, Armache J, Verba K, Cheng Y, Agard D . MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods. 2017; 14(4):331-332. PMC: 5494038. DOI: 10.1038/nmeth.4193. View