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An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. Proc Natl Acad Sci U S A 2020; 117:26226-26236. [PMID: 33028677 DOI: 10.1073/pnas.2013920117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
VCP/p97, an enzyme critical to proteostasis, is regulated through interactions with protein adaptors targeting it to specific cellular tasks. One such adaptor, p47, forms a complex with p97 to direct lipid membrane remodeling. Here, we use NMR and other biophysical methods to study the structural dynamics of p47 and p47-p97 complexes. Disordered regions in p47 are shown to be critical in directing intra-p47 and p47-p97 interactions via a pair of previously unidentified linear motifs. One of these, an SHP domain, regulates p47 binding to p97 in a manner that depends on the nucleotide state of p97. NMR and electron cryomicroscopy data have been used as restraints in molecular dynamics trajectories to develop structural ensembles for p47-p97 complexes in adenosine diphosphate (ADP)- and adenosine triphosphate (ATP)-bound conformations, highlighting differences in interactions in the two states. Our study establishes the importance of intrinsically disordered regions in p47 for the formation of functional p47-p97 complexes.
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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. Conformational changes in the AAA ATPase p97-p47 adaptor complex. EMBO J 2006; 25:1967-76. [PMID: 16601695 PMCID: PMC1456939 DOI: 10.1038/sj.emboj.7601055] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 02/27/2006] [Indexed: 11/08/2022] Open
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.
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Affiliation(s)
- Fabienne Beuron
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Ingrid Dreveny
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Xuemei Yuan
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Valerie E Pye
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Ciaran Mckeown
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Louise C Briggs
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Matthew J Cliff
- Department of Biochemistry and Molecular Biology, University College London, London, UK
| | - Yayoi Kaneko
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- PRESTO and SORST, Japan Science and Technology Corporation, Japan
| | - Russell Wallis
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Infection, Immunity, and Inflammation, Medical Research Council Immunochemistry Unit, University of Leicester, Leicester, UK
| | - Rivka L Isaacson
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - John E Ladbury
- Department of Biochemistry and Molecular Biology, University College London, London, UK
| | - Steve J Matthews
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Hisao Kondo
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- PRESTO and SORST, Japan Science and Technology Corporation, Japan
| | - Xiaodong Zhang
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
| | - Paul S Freemont
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington Campus, Biochemistry Building, South Kensington, London SW7 2AZ, UK. Tel.: +44 20 7594 5327; Fax: +44 20 7594 3057; E-mail:
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Albrecht M, Golatta M, Wüllner U, Lengauer T. Structural and functional analysis of ataxin-2 and ataxin-3. ACTA ACUST UNITED AC 2004; 271:3155-70. [PMID: 15265035 DOI: 10.1111/j.1432-1033.2004.04245.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3) are autosomal-dominantly inherited, neurodegenerative diseases caused by CAG repeat expansions in the coding regions of the genes encoding ataxin-2 and ataxin-3, respectively. To provide a rationale for further functional experiments, we explored the protein architectures of ataxin-2 and ataxin-3. Using structure-based multiple sequence alignments of homologous proteins, we investigated domains, sequence motifs, and interaction partners. Our analyses focused on presumably functional amino acids and the construction of tertiary structure models of the RNA-binding Lsm domain of ataxin-2 and the deubiquitinating Josephin domain of ataxin-3. We also speculate about distant evolutionary relationships of ubiquitin-binding UIM, GAT, UBA and CUE domains and helical ANTH and UBX domain extensions.
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Affiliation(s)
- Mario Albrecht
- Max-Planck-Institute for Informatics, Saarbrücken, Germany.
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Rancour DM, Park S, Knight SD, Bednarek SY. Plant UBX domain-containing protein 1, PUX1, regulates the oligomeric structure and activity of arabidopsis CDC48. J Biol Chem 2004; 279:54264-74. [PMID: 15498773 DOI: 10.1074/jbc.m405498200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p97/CDC48 is a highly abundant hexameric AAA-ATPase that functions as a molecular chaperone in numerous diverse cellular activities. We have identified an Arabidopsis UBX domain-containing protein, PUX1, which functions to regulate the oligomeric structure of the Arabidopsis homolog of p97/CDC48, AtCDC48, as well as mammalian p97. PUX1 is a soluble protein that co-fractionates with non-hexameric AtCDC48 and physically interacts with AtCDC48 in vivo. Binding of PUX1 to AtCDC48 is mediated through the UBX-containing C-terminal domain. However, disassembly of the chaperone is dependent upon the N-terminal domain of PUX1. These findings provide evidence that the assembly and disassembly of the hexameric p97/CDC48 complex is a dynamic process. This new unexpected level of regulation for p97/CDC48 was demonstrated to be critical in vivo as pux1 loss-of-function mutants display accelerated growth relative to wild-type plants. These results suggest a role for AtCDC48 and PUX1 in regulating plant growth.
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Affiliation(s)
- David M Rancour
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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