Home LiteratureArticle Details
PMID: 16601695 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Conformational changes in the AAA ATPase p97-p47 adaptor complex.

The EMBO journal ·Vol. 25 ·No. 9 ·2006-05-03 ·Pages 1967-76

Beuron F, Dreveny I, Yuan X, Pye VE, McKeown C, Briggs LC, Cliff MJ, Kaneko Y, Wallis R, Isaacson RL, Ladbury JE, Matthews SJ, Kondo H, Zhang X, Freemont PS

Abstract

The AAA+ATPase p97/VCP, helped by adaptor proteins, exerts its essential role in cellular events such as endoplasmic reticulum-associated protein degradation or the reassembly of Golgi, ER and the nuclear envelope after mitosis. Here, we report the three-dimensional cryo-electron microscopy structures at approximately 20 Angstroms resolution in two nucleotide states of the endogenous hexameric p97 in complex with a recombinant p47 trimer, one of the major p97 adaptor proteins involved in membrane fusion. Depending on the nucleotide state, we observe the p47 trimer to be in two distinct arrangements on top of the p97 hexamer. By combining the EM data with NMR and other biophysical measurements, we propose a model of ATP-dependent p97(N) domain motions that lead to a rearrangement of p47 domains, which could result in the disassembly of target protein complexes.

MeSH Terms
Adenosine Triphosphatases/chemistry,ultrastructure Adenosine Triphosphate/chemistry Animals Cryoelectron Microscopy Models, Molecular N-Ethylmaleimide-Sensitive Proteins/chemistry,ultrastructure Nuclear Proteins/chemistry,ultrastructure Protein Conformation Protein Structure, Tertiary SNARE Proteins/chemistry Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins/chemistry,ultrastructure
Chemicals
Nuclear Proteins SNARE Proteins Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins Adenosine Triphosphate Adenosine Triphosphatases p97 ATPase N-Ethylmaleimide-Sensitive Proteins
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Beuron Fabienne
Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, UK.
Dreveny Ingrid
Yuan Xuemei
Pye Valerie E
McKeown Ciaran
Briggs Louise C
Cliff Matthew J
Kaneko Yayoi
Wallis Russell
Isaacson Rivka L
Ladbury John E
Matthews Steve J
Kondo Hisao
Zhang Xiaodong
Freemont Paul S
References (43)
43 references, click to expand
  1. Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model.
    J Mol Biol. 2003 Mar 28;327(3):619-29 PMID: 12634057
  2. Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48.
    Nat Cell Biol. 2002 Feb;4(2):134-9 PMID: 11813000
  3. Nucleotide dependent motion and mechanism of action of p97/VCP.
    J Mol Biol. 2005 Mar 25;347(2):437-52 PMID: 15740751
  4. Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-Ray scattering.
    Structure. 2005 Feb;13(2):183-95 PMID: 15698563
  5. Direct binding of ubiquitin conjugates by the mammalian p97 adaptor complexes, p47 and Ufd1-Npl4.
    EMBO J. 2002 Nov 1;21(21):5645-52 PMID: 12411482
  6. Improved methods for building protein models in electron density maps and the location of errors in these models.
    Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9 PMID: 2025413
  7. The crystal structure of murine p97/VCP at 3.6A.
    J Struct Biol. 2003 Dec;144(3):337-48 PMID: 14643202
  8. AAA+ superfamily ATPases: common structure--diverse function.
    Genes Cells. 2001 Jul;6(7):575-97 PMID: 11473577
  9. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains.
    Nat Struct Biol. 2003 Oct;10(10):856-63 PMID: 12949490
  10. NSF/SNAPs and p97/p47/VCIP135 are sequentially required for cell cycle-dependent reformation of the ER network.
    Genes Cells. 2005 Oct;10(10):989-99 PMID: 16164599
  11. NSF and p97/VCP: similar at first, different at last.
    FEBS Lett. 2003 Nov 27;555(1):126-33 PMID: 14630332
  12. The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol.
    Nature. 2001 Dec 6;414(6864):652-6 PMID: 11740563
  13. Structure of the AAA ATPase p97.
    Mol Cell. 2000 Dec;6(6):1473-84 PMID: 11163219
  14. Role of the ubiquitin-selective CDC48(UFD1/NPL4 )chaperone (segregase) in ERAD of OLE1 and other substrates.
    EMBO J. 2002 Feb 15;21(4):615-21 PMID: 11847109
  15. p97 and close encounters of every kind: a brief review.
    Biochem Soc Trans. 2004 Nov;32(Pt 5):715-20 PMID: 15493996
  16. A link between sequence conservation and domain motion within the AAA+ family.
    J Struct Biol. 2004 Apr-May;146(1-2):189-204 PMID: 15037250
  17. The AAA ATPase p97/VCP interacts with its alternative co-factors, Ufd1-Npl4 and p47, through a common bipartite binding mechanism.
    J Biol Chem. 2004 Nov 26;279(48):49609-16 PMID: 15371428
  18. p47 is a cofactor for p97-mediated membrane fusion.
    Nature. 1997 Jul 3;388(6637):75-8 PMID: 9214505
  19. The formation of Golgi stacks from vesiculated Golgi membranes requires two distinct fusion events.
    Cell. 1995 Sep 22;82(6):895-904 PMID: 7553850
  20. The SEP domain of p47 acts as a reversible competitive inhibitor of cathepsin L.
    FEBS Lett. 2004 Oct 22;576(3):358-62 PMID: 15498563
  21. Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.
    EMBO J. 2004 Mar 10;23(5):1030-9 PMID: 14988733
  22. Use of multivariate statistics in analysing the images of biological macromolecules.
    Ultramicroscopy. 1981;6(2):187-94 PMID: 7268930
  23. Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle.
    Nat Struct Biol. 2002 Dec;9(12):950-7 PMID: 12434150
  24. Golgi reassembly after mitosis: the AAA family meets the ubiquitin family.
    Biochim Biophys Acta. 2005 Jun 30;1744(2):108-19 PMID: 15878210
  25. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction.
    Ultramicroscopy. 1987;21(2):111-23 PMID: 12425301
  26. A major conformational change in p97 AAA ATPase upon ATP binding.
    Mol Cell. 2000 Dec;6(6):1485-90 PMID: 11163220
  27. VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo.
    J Cell Biol. 2002 Dec 9;159(5):855-66 PMID: 12473691
  28. Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 A resolution by electron cryomicroscopy and angular reconstitution.
    J Mol Biol. 1997 Aug 22;271(3):417-37 PMID: 9268669
  29. Distinct AAA-ATPase p97 complexes function in discrete steps of nuclear assembly.
    Nat Cell Biol. 2001 Dec;3(12):1086-91 PMID: 11781570
  30. Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
    EMBO J. 2003 Sep 1;22(17):4365-74 PMID: 12941689
  31. Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97.
    EMBO J. 2004 Apr 7;23(7):1463-73 PMID: 15029246
  32. A new generation of the IMAGIC image processing system.
    J Struct Biol. 1996 Jan-Feb;116(1):17-24 PMID: 8742718
  33. Syntaxin 5 is a common component of the NSF- and p97-mediated reassembly pathways of Golgi cisternae from mitotic Golgi fragments in vitro.
    Cell. 1998 Mar 6;92(5):603-10 PMID: 9506515
  34. The AAA-ATPase Cdc48/p97 regulates spindle disassembly at the end of mitosis.
    Cell. 2003 Oct 31;115(3):355-67 PMID: 14636562
  35. HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins.
    Mol Biol Cell. 2001 Dec;12(12):4114-28 PMID: 11739805
  36. The Ubx2 and Ubx3 cofactors direct Cdc48 activity to proteolytic and nonproteolytic ubiquitin-dependent processes.
    Curr Biol. 2004 May 4;14(9):824-8 PMID: 15120077
  37. Complete backbone resonance assignments of p47: the 41kDa adaptor protein of the AAA ATPase p97.
    J Biomol NMR. 2004 Mar;28(3):309-10 PMID: 14752269
  38. Solution structure and interaction surface of the C-terminal domain from p47: a major p97-cofactor involved in SNARE disassembly.
    J Mol Biol. 2001 Aug 10;311(2):255-63 PMID: 11478859
  39. Fourier shell correlation threshold criteria.
    J Struct Biol. 2005 Sep;151(3):250-62 PMID: 16125414
  40. p97/p47-Mediated biogenesis of Golgi and ER.
    J Biochem. 2005 Feb;137(2):115-9 PMID: 15749824
  41. Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains.
    J Cell Biol. 2003 Jul 7;162(1):71-84 PMID: 12847084
  42. Geometry-based flexible and symmetric protein docking.
    Proteins. 2005 Aug 1;60(2):224-31 PMID: 15981269
  43. Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin-dependent protein degradation.
    EMBO Rep. 2004 Aug;5(8):818-24 PMID: 15258615
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1038/sj.emboj.7601055
Published
2006-05-03
Epub
2006-00-06
Pages
1967-76
Language
English
Region
England
NLM ID
8208664
PMCID
PMC1456939
Subset
IM
Grants
Wellcome Trust · 085464 · United Kingdom
Wellcome Trust · 073908 · United Kingdom
NIBIB NIH HHS · 5 P41 EB2181 · United States
NIBIB NIH HHS · P41 EB002181 · United States
Medical Research Council · MC_U117533887 · United Kingdom
External Links
PubMed source DOI: 10.1038/sj.emboj.7601055 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2