51
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The AAA+ ATPase p97, a cellular multitool. Biochem J 2017; 474:2953-2976. [PMID: 28819009 PMCID: PMC5559722 DOI: 10.1042/bcj20160783] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 12/17/2022]
Abstract
The AAA+ (ATPases associated with diverse cellular activities) ATPase p97 is essential to a wide range of cellular functions, including endoplasmic reticulum-associated degradation, membrane fusion, NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation and chromatin-associated processes, which are regulated by ubiquitination. p97 acts downstream from ubiquitin signaling events and utilizes the energy from ATP hydrolysis to extract its substrate proteins from cellular structures or multiprotein complexes. A multitude of p97 cofactors have evolved which are essential to p97 function. Ubiquitin-interacting domains and p97-binding domains combine to form bi-functional cofactors, whose complexes with p97 enable the enzyme to interact with a wide range of ubiquitinated substrates. A set of mutations in p97 have been shown to cause the multisystem proteinopathy inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia. In addition, p97 inhibition has been identified as a promising approach to provoke proteotoxic stress in tumors. In this review, we will describe the cellular processes governed by p97, how the cofactors interact with both p97 and its ubiquitinated substrates, p97 enzymology and the current status in developing p97 inhibitors for cancer therapy.
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52
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Abstract
A conserved AAA+ ATPase, called Cdc48 in yeast and p97 or VCP in metazoans, plays an essential role in many cellular processes by segregating polyubiquitinated proteins from complexes or membranes. For example, in endoplasmic reticulum (ER)-associated protein degradation (ERAD), Cdc48/p97 pulls polyubiquitinated, misfolded proteins out of the ER and transfers them to the proteasome. Cdc48/p97 consists of an N-terminal domain and two ATPase domains (D1 and D2). Six Cdc48 monomers form a double-ring structure surrounding a central pore. Cdc48/p97 cooperates with a number of different cofactors, which bind either to the N-terminal domain or to the C-terminal tail. The mechanism of Cdc48/p97 action is poorly understood, despite its critical role in many cellular systems. Recent in vitro experiments using yeast Cdc48 and its heterodimeric cofactor Ufd1/Npl4 (UN) have resulted in novel mechanistic insight. After interaction of the substrate-attached polyubiquitin chain with UN, Cdc48 uses ATP hydrolysis in the D2 domain to move the polypeptide through its central pore, thereby unfolding the substrate. ATP hydrolysis in the D1 domain is involved in substrate release from the Cdc48 complex, which requires the cooperation of the ATPase with a deubiquitinase (DUB). Surprisingly, the DUB does not completely remove all ubiquitin molecules; the remaining oligoubiquitin chain is also translocated through the pore. Cdc48 action bears similarities to the translocation mechanisms employed by bacterial AAA ATPases and the eukaryotic 19S subunit of the proteasome, but differs significantly from that of a related type II ATPase, the NEM-sensitive fusion protein (NSF). Many questions about Cdc48/p97 remain unanswered, including how it handles well-folded substrate proteins, how it passes substrates to the proteasome, and how various cofactors modify substrates and regulate its function.
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Affiliation(s)
- Nicholas Bodnar
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Tom Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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53
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Exploiting conformational plasticity in the AAA+ protein VCP/p97 to modify function. Proc Natl Acad Sci U S A 2017; 114:E6822-E6829. [PMID: 28760999 DOI: 10.1073/pnas.1707974114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
p97/VCP, a member of the AAA+ (ATPases associated with diverse cellular activities) family of proteins, is implicated in the etiology of a group of degenerative diseases affecting bone and muscle tissue as well as the central nervous system. Methyl-TROSY-based NMR studies have previously revealed how disease-causing mutations deregulate a subtle dynamic conformational equilibrium involving the N-terminal domain (NTD) with implications for the binding of certain adaptors, providing insight into how disease mutations lead to abnormal function. Herein the conformational plasticity of the p97 system is explored in an attempt to identify hotspots that can serve as targets for restoring function in disease mutants by shifting the position of the NTD back to its wild-type location. Although p97 is overall robust with respect to extensive mutagenesis throughout the protein involving conservative substitutions of hydrophobic residues, key positions have been identified that alter the NTD equilibrium; these lie in specific regions that localize to the interface between the NTD and the D1 nucleotide-binding domain of the complex. Notably, for a severe disease mutant involving an R155C substitution the NTD equilibrium can be shifted back to its wild-type position by mutation at a secondary site with restoration of wild-type two-pronged binding of the UBXD1 adaptor protein that is impaired in disease; this underlies the potential for recovering function by targeting p97 disease mutants with drug molecules.
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54
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Tillotson J, Zerio CJ, Harder B, Ambrose AJ, Jung KS, Kang M, Zhang DD, Chapman E. Arsenic Compromises Both p97 and Proteasome Functions. Chem Res Toxicol 2017; 30:1508-1514. [PMID: 28636814 PMCID: PMC5687067 DOI: 10.1021/acs.chemrestox.7b00158] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Exposure to arsenic is a worldwide problem that affects more than 200 million people. The underlying mechanisms of arsenic toxicity have been difficult to ascertain due to arsenic's pleotropic effects. A number of recent investigations have shown that arsenic can compromise protein quality control through the ubiquitin proteasome system (UPS) or the endoplasmic reticulum associated protein degradation (ERAD) pathway. In this article, a link between arsenic and protein quality control is reported. Biochemical and cellular data demonstrate a misregulation of the ATPase cycle of the ATPase associated with various cellular activities (AAA+) chaperone, p97. Interestingly, the loss of p97 activity is due to the increased rate of ATP hydrolysis, which mimics a collection of pathogenic genetic p97 lesions. Cellular studies, using a well characterized reporter of both the proteasome and p97, show the proteasome to also be compromised. This loss of both p97 and proteasome functions can explain the catastrophic protein quality control issues observed in acute, high level arsenic exposures.
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Affiliation(s)
| | | | | | | | | | | | - Donna D. Zhang
- Corresponding Authors: (D.D.Z.) University of Arizona, Department of Pharmacology and Toxicology, College of Pharmacy, 1703 East Mabel St., P.O. Box 210119, Tucson, AZ, USA 85721-0119. Tel: 520-626-9918. .; (E.C.) University of Arizona, Department of Pharmacology and Toxicology, College of Pharmacy, 1703 East Mabel St., P.O. Box 210119, Tucson, AZ, USA 85721-0207. Tel: 520-626-2740.
| | - Eli Chapman
- Corresponding Authors: (D.D.Z.) University of Arizona, Department of Pharmacology and Toxicology, College of Pharmacy, 1703 East Mabel St., P.O. Box 210119, Tucson, AZ, USA 85721-0119. Tel: 520-626-9918. .; (E.C.) University of Arizona, Department of Pharmacology and Toxicology, College of Pharmacy, 1703 East Mabel St., P.O. Box 210119, Tucson, AZ, USA 85721-0207. Tel: 520-626-2740.
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55
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Ye Y, Tang WK, Zhang T, Xia D. A Mighty "Protein Extractor" of the Cell: Structure and Function of the p97/CDC48 ATPase. Front Mol Biosci 2017; 4:39. [PMID: 28660197 PMCID: PMC5468458 DOI: 10.3389/fmolb.2017.00039] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 12/13/2022] Open
Abstract
p97/VCP (known as Cdc48 in S. cerevisiae or TER94 in Drosophila) is one of the most abundant cytosolic ATPases. It is highly conserved from archaebacteria to eukaryotes. In conjunction with a large number of cofactors and adaptors, it couples ATP hydrolysis to segregation of polypeptides from immobile cellular structures such as protein assemblies, membranes, ribosome, and chromatin. This often results in proteasomal degradation of extracted polypeptides. Given the diversity of p97 substrates, this "segregase" activity has profound influence on cellular physiology ranging from protein homeostasis to DNA lesion sensing, and mutations in p97 have been linked to several human diseases. Here we summarize our current understanding of the structure and function of this important cellular machinery and discuss the relevant clinical implications.
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Affiliation(s)
- Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
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56
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Saffert P, Enenkel C, Wendler P. Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes. Front Mol Biosci 2017; 4:33. [PMID: 28611990 PMCID: PMC5447069 DOI: 10.3389/fmolb.2017.00033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/05/2017] [Indexed: 12/16/2022] Open
Abstract
Protein complexes of the Type II AAA+ (ATPases associated with diverse cellular activities) family are typically hexamers of 80–150 kDa protomers that harbor two AAA+ ATPase domains. They form double ring assemblies flanked by associated domains, which can be N-terminal, intercalated or C-terminal to the ATPase domains. Most prominent members of this family include NSF (N-ethyl-maleimide sensitive factor), p97/VCP (valosin-containing protein), the Pex1/Pex6 complex and Hsp104 in eukaryotes and ClpB in bacteria. Tremendous efforts have been undertaken to understand the conformational dynamics of protein remodeling type II AAA+ complexes. A uniform mode of action has not been derived from these works. This review focuses on p97/VCP and the Pex1/6 complex, which both structurally remodel ubiquitinated substrate proteins. P97/VCP plays a role in many processes, including ER- associated protein degradation, and the Pex1/Pex6 complex dislocates and recycles the transport receptor Pex5 from the peroxisomal membrane during peroxisomal protein import. We give an introduction into existing knowledge about the biochemical and cellular activities of the complexes before discussing structural information. We particularly emphasize recent electron microscopy structures of the two AAA+ complexes and summarize their structural differences.
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Affiliation(s)
- Paul Saffert
- Department of Biochemistry, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
| | - Cordula Enenkel
- Department of Biochemistry, University of TorontoToronto, ON, Canada
| | - Petra Wendler
- Department of Biochemistry, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
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57
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Ubiquitin- and ATP-dependent unfoldase activity of P97/VCP•NPLOC4•UFD1L is enhanced by a mutation that causes multisystem proteinopathy. Proc Natl Acad Sci U S A 2017; 114:E4380-E4388. [PMID: 28512218 DOI: 10.1073/pnas.1706205114] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
p97 is a "segregase" that plays a key role in numerous ubiquitin (Ub)-dependent pathways such as ER-associated degradation. It has been hypothesized that p97 extracts proteins from membranes or macromolecular complexes to enable their proteasomal degradation; however, the complex nature of p97 substrates has made it difficult to directly observe the fundamental basis for this activity. To address this issue, we developed a soluble p97 substrate-Ub-GFP modified with K48-linked ubiquitin chains-for in vitro p97 activity assays. We demonstrate that WT p97 can unfold proteins and that this activity is dependent on the p97 adaptor NPLOC4-UFD1L, ATP hydrolysis, and substrate ubiquitination, with branched chains providing maximal stimulation. Furthermore, we show that a p97 mutant that causes inclusion body myopathy, Paget's disease of bone, and frontotemporal dementia in humans unfolds substrate faster, suggesting that excess activity may underlie pathogenesis. This work overcomes a significant barrier in the study of p97 and will allow the future dissection of p97 mechanism at a level of detail previously unattainable.
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58
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Hänzelmann 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. [PMID: 28451587 PMCID: PMC5389986 DOI: 10.3389/fmolb.2017.00021] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric type II AAA ATPase (ATPase associated with various activities) p97 (also referred to as VCP, Cdc48, and Ter94) is critically involved in a variety of cellular activities including pathways such as DNA replication and repair which both involve chromatin remodeling, and is a key player in various protein quality control pathways mediated by the ubiquitin proteasome system as well as autophagy. Correspondingly, p97 has been linked to various pathophysiological states including cancer, neurodegeneration, and premature aging. p97 encompasses an N-terminal domain, two highly conserved ATPase domains and an unstructured C-terminal tail. This enzyme hydrolyzes ATP and utilizes the resulting energy to extract or disassemble protein targets modified with ubiquitin from stable protein assemblies, chromatin and membranes. p97 participates in highly diverse cellular processes and hence its activity is tightly controlled. This is achieved by multiple regulatory cofactors, which either associate with the N-terminal domain or interact with the extreme C-terminus via distinct binding elements and target p97 to specific cellular pathways, sometimes requiring the simultaneous association with more than one cofactor. Most cofactors are recruited to p97 through conserved binding motifs/domains and assist in substrate recognition or processing by providing additional molecular properties. A tight control of p97 cofactor specificity and diversity as well as the assembly of higher-order p97-cofactor complexes is accomplished by various regulatory mechanisms, which include bipartite binding, binding site competition, changes in oligomeric assemblies, and nucleotide-induced conformational changes. Furthermore, post-translational modifications (PTMs) like acetylation, palmitoylation, phosphorylation, SUMOylation, and ubiquitylation of p97 have been reported which further modulate its diverse molecular activities. In this review, we will describe the molecular basis of p97-cofactor specificity/diversity and will discuss how PTMs can modulate p97-cofactor interactions and affect the physiological and patho-physiological functions of p97.
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Affiliation(s)
- Petra Hänzelmann
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
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59
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Zhang T, Mishra P, Hay BA, Chan D, Guo M. Valosin-containing protein (VCP/p97) inhibitors relieve Mitofusin-dependent mitochondrial defects due to VCP disease mutants. eLife 2017; 6. [PMID: 28322724 PMCID: PMC5360448 DOI: 10.7554/elife.17834] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022] Open
Abstract
Missense mutations of valosin-containing protein (VCP) cause an autosomal dominant disease known as inclusion body myopathy, Paget disease with frontotemporal dementia (IBMPFD) and other neurodegenerative disorders. The pathological mechanism of IBMPFD is not clear and there is no treatment. We show that endogenous VCP negatively regulates Mitofusin, which is required for outer mitochondrial membrane fusion. Because 90% of IBMPFD patients have myopathy, we generated an in vivo IBMPFD model in adult Drosophila muscle, which recapitulates disease pathologies. We show that common VCP disease mutants act as hyperactive alleles with respect to regulation of Mitofusin. Importantly, VCP inhibitors suppress mitochondrial defects, muscle tissue damage and cell death associated with IBMPFD models in Drosophila. These inhibitors also suppress mitochondrial fusion and respiratory defects in IBMPFD patient fibroblasts. These results suggest that VCP disease mutants cause IBMPFD through a gain-of-function mechanism, and that VCP inhibitors have therapeutic value.
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Affiliation(s)
- Ting Zhang
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angele, United States
| | - Prashant Mishra
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - David Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ming Guo
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angele, United States.,Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, University of California, Los Angeles, United States
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60
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A conserved inter-domain communication mechanism regulates the ATPase activity of the AAA-protein Drg1. Sci Rep 2017; 7:44751. [PMID: 28303975 PMCID: PMC5356007 DOI: 10.1038/srep44751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/13/2017] [Indexed: 11/14/2022] Open
Abstract
AAA-ATPases fulfil essential roles in different cellular pathways and often act in form of hexameric complexes. Interaction with pathway-specific substrate and adaptor proteins recruits them to their targets and modulates their catalytic activity. This substrate dependent regulation of ATP hydrolysis in the AAA-domains is mediated by a non-catalytic N-terminal domain. The exact mechanisms that transmit the signal from the N-domain and coordinate the individual AAA-domains in the hexameric complex are still the topic of intensive research. Here, we present the characterization of a novel mutant variant of the eukaryotic AAA-ATPase Drg1 that shows dysregulation of ATPase activity and altered interaction with Rlp24, its substrate in ribosome biogenesis. This defective regulation is the consequence of amino acid exchanges at the interface between the regulatory N-domain and the adjacent D1 AAA-domain. The effects caused by these mutations strongly resemble those of pathological mutations of the AAA-ATPase p97 which cause the hereditary proteinopathy IBMPFD (inclusion body myopathy associated with Paget’s disease of the bone and frontotemporal dementia). Our results therefore suggest well conserved mechanisms of regulation between structurally, but not functionally related members of the AAA-family.
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61
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Tang WK, Xia D. Mutations in the Human AAA + Chaperone p97 and Related Diseases. Front Mol Biosci 2016; 3:79. [PMID: 27990419 PMCID: PMC5131264 DOI: 10.3389/fmolb.2016.00079] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
A number of neurodegenerative diseases have been linked to mutations in the human protein p97, an abundant cytosolic AAA+ (ATPase associated with various cellular activities) ATPase, that functions in a large number of cellular pathways. With the assistance of a variety of cofactors and adaptor proteins, p97 couples the energy of ATP hydrolysis to conformational changes that are necessary for its function. Disease-linked mutations, which are found at the interface between two main domains of p97, have been shown to alter the function of the protein, although the pathogenic mutations do not appear to alter the structure of individual subunit of p97 or the formation of the hexameric biological unit. While exactly how pathogenic mutations alter the cellular function of p97 remains unknown, functional, biochemical and structural differences between wild-type and pathogenic mutants of p97 are being identified. Here, we summarize recent progress in the study of p97 pathogenic mutants.
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Affiliation(s)
- Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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62
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Yeo BK, Yu SW. Valosin-containing protein (VCP): structure, functions, and implications in neurodegenerative diseases. Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1259181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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63
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Schuetz AK, Kay LE. A Dynamic molecular basis for malfunction in disease mutants of p97/VCP. eLife 2016; 5. [PMID: 27828775 PMCID: PMC5102582 DOI: 10.7554/elife.20143] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/25/2016] [Indexed: 12/04/2022] Open
Abstract
p97/VCP is an essential, abundant AAA+ ATPase that is conserved throughout eukaryotes, with central functions in diverse processes ranging from protein degradation to DNA damage repair and membrane fusion. p97 has been implicated in the etiology of degenerative diseases and in cancer. Using Nuclear Magnetic Resonance spectroscopy we reveal how disease-causing mutations in p97 deregulate dynamics of the N-terminal domain that binds adaptor proteins involved in controlling p97 function. Our results provide a molecular basis for understanding how malfunction occurs whereby mutations shift the ADP-bound form of the enzyme towards an ATP-like state in a manner that correlates with disease severity. This deregulation interferes with the two-pronged binding of an adaptor that affects p97 function in lysosomal degradation of substrates. Subtle structural changes propagate from mutation sites to regions distal in space, defining allosteric networks that facilitate inter-domain communication, with potential implications for modulation of enzyme activity by drug molecules. DOI:http://dx.doi.org/10.7554/eLife.20143.001
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Affiliation(s)
- Anne K Schuetz
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Cananda.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Cananda.,Department of Chemistry, University of Toronto, Toronto, Canada.,Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
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64
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Arumughan A, Roske Y, Barth C, Forero LL, Bravo-Rodriguez K, Redel A, Kostova S, McShane E, Opitz R, Faelber K, Rau K, Mielke T, Daumke O, Selbach M, Sanchez-Garcia E, Rocks O, Panáková D, Heinemann U, Wanker EE. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers. Nat Commun 2016; 7:13047. [PMID: 27762274 PMCID: PMC5080433 DOI: 10.1038/ncomms13047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity. The AAA+ ATPase p97 is an essential hexameric protein with multiple protein interaction partners and cellular functions. Here, the authors use interaction mapping to examine partner proteins of this large complex, and assess the effects of these proteins on the disassembly of the p97 complex.
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Affiliation(s)
- Anup Arumughan
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Carolin Barth
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Laura Lleras Forero
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kenny Bravo-Rodriguez
- Max-Planck-Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexandra Redel
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Simona Kostova
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Erik McShane
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Robert Opitz
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Katja Faelber
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Kirstin Rau
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14194 Berlin, Germany
| | - Oliver Daumke
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Elsa Sanchez-Garcia
- Max-Planck-Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Oliver Rocks
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
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65
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Bulfer SL, Chou TF, Arkin MR. p97 Disease Mutations Modulate Nucleotide-Induced Conformation to Alter Protein-Protein Interactions. ACS Chem Biol 2016; 11:2112-6. [PMID: 27267671 PMCID: PMC5224236 DOI: 10.1021/acschembio.6b00350] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
The AAA+ ATPase p97/VCP
adopts at least three conformations that
depend on the binding of ADP and ATP and alter the orientation of
the N-terminal protein–protein interaction (PPI) domain into
“up” and “down” conformations. Point mutations
that cause multisystem proteinopathy 1 (MSP1) are found at the interface
of the N domain and D1-ATPase domain and potentially alter the conformational
preferences of p97. Additionally, binding of “adaptor”
proteins to the N-domain regulates p97’s catalytic activity.
We propose that p97/adaptor PPIs are coupled to p97 conformational
states. We evaluated the binding of nucleotides and the adaptor proteins
p37 and p47 to wild-type p97 and MSP1 mutants. Notably, p47 and p37
bind 8-fold more weakly to the ADP-bound conformation of wild-type
p97 compared to the ATP-bound conformation. However, MSP1 mutants
lose this nucleotide-induced conformational coupling because they
destabilize the ADP-bound, “down” conformation of the
N-domain. Loss in conformation coupling to PPIs could contribute to
the mechanism of MSP1.
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Affiliation(s)
- Stacie L. Bulfer
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94143, United States
| | - Tsui-Fen Chou
- Division
of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, California 90502, United States
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94143, United States
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Xue L, Blythe EE, Freiberger EC, Mamrosh JL, Hebert AS, Reitsma JM, Hess S, Coon JJ, Deshaies RJ. Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor. Mol Cell Proteomics 2016; 15:2970-86. [PMID: 27406709 DOI: 10.1074/mcp.m116.061036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 11/06/2022] Open
Abstract
Protein quality control (PQC) plays an important role in stemming neurodegenerative diseases and is essential for the growth of some cancers. Valosin-containing protein (VCP)/p97 plays a pivotal role in multiple PQC pathways by interacting with numerous adaptors that link VCP to specific PQC pathways and substrates and influence the post-translational modification state of substrates. However, our poor understanding of the specificity and architecture of the adaptors, and the dynamic properties of their interactions with VCP hinders our understanding of fundamental features of PQC and how modulation of VCP activity can best be exploited therapeutically. In this study we use multiple mass spectrometry-based proteomic approaches combined with biophysical studies to characterize the interaction of adaptors with VCP. Our results reveal that most VCP-adaptor interactions are characterized by rapid dynamics that in some cases are modulated by the VCP inhibitor NMS873. These findings have significant implications for both the regulation of VCP function and the impact of VCP inhibition on different VCP-adaptor complexes.
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Affiliation(s)
- Liang Xue
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | - Emily E Blythe
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | - Elyse C Freiberger
- §Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jennifer L Mamrosh
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | | | - Justin M Reitsma
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | - Sonja Hess
- **Proteome Exploration Laboratory (PEL), Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Joshua J Coon
- §Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ¶Genome Center of Wisconsin, 425 Henry Mall, Madison, Wisconsin 53706; ‖Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Raymond J Deshaies
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125; ‡‡Howard Hughes Medical Institute, Pasadena, California 91125
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67
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Xia D, Tang WK, Ye Y. Structure and function of the AAA+ ATPase p97/Cdc48p. Gene 2016. [DOI: 10.1016/j.gene.2016.02.042 and 21=21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2022]
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68
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Xia D, Tang WK, Ye Y. Structure and function of the AAA+ ATPase p97/Cdc48p. Gene 2016. [DOI: 10.1016/j.gene.2016.02.042 and 67=89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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69
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Rijal R, Arhzaouy K, Strucksberg KH, Cross M, Hofmann A, Schröder R, Clemen CS, Eichinger L. Mutant p97 exhibits species-specific changes of its ATPase activity and compromises the UBXD9-mediated monomerisation of p97 hexamers. Eur J Cell Biol 2016; 95:195-207. [PMID: 27132113 DOI: 10.1016/j.ejcb.2016.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022] Open
Abstract
p97 (VCP) is a homo-hexameric triple-A ATPase that exerts a plethora of cellular processes. Heterozygous missense mutations of p97 cause at least five human neurodegenerative disorders. However, the specific molecular consequences of p97 mutations are hitherto widely unknown. Our in silico structural models of human and Dictyostelium p97 showed that the disease-causing human R93C, R155H, and R155C as well as Dictyostelium R154C, E219K, R154C/E219K p97 mutations constitute variations in surface-exposed locations. In-gel ATPase activity measurements of p97 monomers and hexamers revealed significant mutation- and species-specific differences. While all human p97 mutations led to an increase in ATPase activity, no changes could be detected for the Dictyostelium R154C mutant, which is orthologous to human R155C. The E219K mutation led to an almost complete loss of activity, which was partially recuperated in the R154C/E219K double-mutant indicating p97 inter-domain communication. By means of co-immunoprecipitation experiments we identified an UBX-domain containing Dictyostelium protein as a novel p97 interaction partner. We categorized all UBX-domain containing Dictyostelium proteins and named the interaction partner UBXD9. Pull-down assays and surface plasmon resonance analyses of Dictyostelium UBXD9 or the human orthologue TUG/ASPL/UBXD9 demonstrated direct interactions with p97 as well as species-, mutation- and ATP-dependent differences in the binding affinities. Sucrose density gradient assays revealed that both human and Dictyostelium UBXD9 proteins very efficiently disassembled wild-type, but to a lesser extent mutant p97 hexamers into monomers. Our results are consistent with a scenario in which p97 point mutations lead to differences in enzymatic activities and molecular interactions, which in the long-term result in a late-onset and progressive multisystem disease.
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Affiliation(s)
- Ramesh Rijal
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Khalid Arhzaouy
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Karl-Heinz Strucksberg
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Megan Cross
- Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia
| | - Andreas Hofmann
- Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3030, Australia
| | - Rolf Schröder
- Institute of Neuropathology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Christoph S Clemen
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany.
| | - Ludwig Eichinger
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany.
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70
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Xia D, Tang WK, Ye Y. Structure and function of the AAA+ ATPase p97/Cdc48p. Gene 2016; 583:64-77. [PMID: 26945625 DOI: 10.1016/j.gene.2016.02.042] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/29/2022]
Abstract
p97 (also known as valosin-containing protein (VCP) in mammals or Cdc48p in Saccharomyces cerevisiae) is an evolutionarily conserved ATPase present in all eukaryotes and archaebacteria. In conjunction with a collection of cofactors and adaptors, p97/Cdc48p performs an array of biological functions mostly through modulating the stability of 'client' proteins. Using energy from ATP hydrolysis, p97/Cdc48p segregates these molecules from immobile cellular structures such as protein assemblies, membrane organelles, and chromatin. Consequently, the released polypeptides can be efficiently degraded by the ubiquitin proteasome system or recycled. This review summarizes our current understanding of the structure and function of this essential cellular chaperoning system.
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Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States.
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71
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Banerjee S, Bartesaghi A, Merk A, Rao P, Bulfer SL, Yan Y, Green N, Mroczkowski B, Neitz RJ, Wipf P, Falconieri V, Deshaies RJ, Milne JLS, Huryn D, Arkin M, Subramaniam S. 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 2016; 351:871-5. [PMID: 26822609 PMCID: PMC6946184 DOI: 10.1126/science.aad7974] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/14/2016] [Indexed: 12/13/2022]
Abstract
p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2.3 and 2.4 angstroms, respectively. We also report cryo-EM structures (at resolutions of ~3.3, 3.2, and 3.3 angstroms, respectively) for three distinct, coexisting functional states of p97 with occupancies of zero, one, or two molecules of adenosine 5'-O-(3-thiotriphosphate) (ATPγS) per protomer. A large corkscrew-like change in molecular architecture, coupled with upward displacement of the N-terminal domain, is observed only when ATPγS is bound to both the D1 and D2 domains of the protomer. These cryo-EM structures establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution. They also enable elucidation of the binding mode of an allosteric small-molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between the D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function.
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Affiliation(s)
- Soojay Banerjee
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan Merk
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Prashant Rao
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stacie L Bulfer
- Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Yongzhao Yan
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Neal Green
- Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Barbara Mroczkowski
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - R Jeffrey Neitz
- Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91107, USA
| | | | - Donna Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michelle Arkin
- Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA.
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72
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73
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Hänzelmann P, Schindelin H. Structural Basis of ATP Hydrolysis and Intersubunit Signaling in the AAA+ ATPase p97. Structure 2015; 24:127-139. [PMID: 26712278 DOI: 10.1016/j.str.2015.10.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 11/26/2022]
Abstract
p97 belongs to the superfamily of AAA+ ATPases and is characterized by a tandem AAA module, an N-terminal domain involved in substrate and cofactor interactions, and a functionally important unstructured C-terminal tail. The ATPase activity is controlled by an intradomain communication within the same protomer and an interdomain communication between neighboring protomers. Here, we present for the first time crystal structures in which the physiologically relevant p97 hexamer constitutes the content of the asymmetric unit, namely in the apo state without nucleotide in either the D1 or D2 module and in the pre-activated state with ATPγS bound to both modules. The structures provide new mechanistic insights into the interdomain communication mediated by conformational changes of the C terminus as well as an intersubunit signaling network, which couples the nucleotide state to the conformation of the central putative substrate binding pore.
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Affiliation(s)
- Petra Hänzelmann
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
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74
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Fusser M, Kernstock S, Aileni VK, Egge-Jacobsen W, Falnes PØ, Klungland A. Lysine Methylation of the Valosin-Containing Protein (VCP) Is Dispensable for Development and Survival of Mice. PLoS One 2015; 10:e0141472. [PMID: 26544960 PMCID: PMC4636187 DOI: 10.1371/journal.pone.0141472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 10/08/2015] [Indexed: 01/02/2023] Open
Abstract
Valosin-containing protein (VCP) is a homohexameric ATPase involved in a multitude cellular processes and it was recently shown that VCP is trimethylated at lysine 315 by the VCP lysine methyltransferase (VCPKMT). Here, we generated and validated a constitutive knockout mouse by targeting exon 1-4 of the Vcpkmt gene. We show that Vcpkmt is ubiquitously expressed in all tissues examined and confirm the sub-cellular localization to the cytoplasm. We show by (I) mass spectrometric analysis, (II) VCPKMT-mediated in vitro methylation of VCP in cell extracts and (III) immunostaining with a methylation specific antibody, that in Vcpkmt-/- mice the methylation of lysine 315 in VCP is completely abolished. In contrast, VCP is almost exclusively trimethylated in wild-type mice. Furthermore, we investigated the specificity of VCPKMT with in vitro methylation assays using as source of substrate protein extracts from Vcpkmt-/- mouse organs or three human Vcpkmt-/- cell lines. The results show that VCPKMT is a highly specific enzyme, and suggest that VCP is its sole substrate. The Vcpkmt-/- mice were viable, fertile and had no obvious pathological phenotype. Their body weight, life span and acute endurance capacity were comparable to wild-type controls. Overall the results show that VCPKMT is an enzyme required for methylation of K315 of VCP in vivo, but VCPKMT is not essential for development or survival under unstressed conditions.
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Affiliation(s)
- Markus Fusser
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Stefan Kernstock
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Vinay Kumar Aileni
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Wolfgang Egge-Jacobsen
- Glyconor Mass Spectrometry, Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pål Ø. Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- * E-mail:
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75
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Mountassif D, Fabre L, Zaid Y, Halawani D, Rouiller I. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring. Biochem Biophys Res Commun 2015; 468:636-41. [PMID: 26549226 DOI: 10.1016/j.bbrc.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/02/2015] [Indexed: 11/25/2022]
Abstract
Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring.
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Affiliation(s)
- Driss Mountassif
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Lucien Fabre
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Younes Zaid
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Dalia Halawani
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195, USA
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada.
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76
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Trusch F, Matena A, Vuk M, Koerver L, Knævelsrud H, Freemont PS, Meyer H, Bayer P. The N-terminal Region of the Ubiquitin Regulatory X (UBX) Domain-containing Protein 1 (UBXD1) Modulates Interdomain Communication within the Valosin-containing Protein p97. J Biol Chem 2015; 290:29414-27. [PMID: 26475856 DOI: 10.1074/jbc.m115.680686] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 12/15/2022] Open
Abstract
Valosin-containing protein/p97 is an ATP-driven protein segregase that cooperates with distinct protein cofactors to control various aspects of cellular homeostasis. Mutations at the interface between the regulatory N-domain and the first of two ATPase domains (D1 and D2) deregulate the ATPase activity and cause a multisystem degenerative disorder, inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia/amyotrophic lateral sclerosis. Intriguingly, the mutations affect only a subset of p97-mediated pathways correlating with unbalanced cofactor interactions and most prominently compromised binding of the ubiquitin regulatory X domain-containing protein 1 (UBXD1) cofactor during endolysosomal sorting of caveolin-1. However, how the mutations impinge on the p97-cofactor interplay is unclear so far. In cell-based endosomal localization studies, we identified a critical role of the N-terminal region of UBXD1 (UBXD1-N). Biophysical studies using NMR and CD spectroscopy revealed that UBXD1-N can be classified as intrinsically disordered. NMR titration experiments confirmed a valosin-containing protein/p97 interaction motif and identified a second binding site at helices 1 and 2 of UBXD1-N as binding interfaces for p97. In reverse titration experiments, we identified two distant epitopes on the p97 N-domain that include disease-associated residues and an additional interaction between UBXD1-N and the D1D2 barrel of p97 that was confirmed by fluorescence anisotropy. Functionally, binding of UBXD1-N to p97 led to a reduction of ATPase activity and partial protection from proteolysis. These findings indicate that UBXD1-N intercalates into the p97-ND1 interface, thereby modulating interdomain communication of p97 domains and its activity with relevance for disease pathogenesis. We propose that the polyvalent binding mode characterized for UBXD1-N is a more general principle that defines a subset of p97 cofactors.
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Affiliation(s)
| | - Anja Matena
- From Structural and Medicinal Biochemistry and
| | - Maja Vuk
- Molecular Biology I, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany and
| | - Lisa Koerver
- Molecular Biology I, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany and
| | - Helene Knævelsrud
- Molecular Biology I, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany and
| | - Paul S Freemont
- Department of Medicine, Section of Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hemmo Meyer
- Molecular Biology I, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany and
| | - Peter Bayer
- From Structural and Medicinal Biochemistry and
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77
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Control of p97 function by cofactor binding. FEBS Lett 2015; 589:2578-89. [PMID: 26320413 DOI: 10.1016/j.febslet.2015.08.028] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 08/18/2015] [Accepted: 08/18/2015] [Indexed: 12/14/2022]
Abstract
p97 (also known as Cdc48, Ter94, and VCP) is an essential, abundant and highly conserved ATPase driving the turnover of ubiquitylated proteins in eukaryotes. Even though p97 is involved in highly diverse cellular pathways and processes, it exhibits hardly any substrate specificity on its own. Instead, it relies on a large number of regulatory cofactors controlling substrate specificity and turnover. The complexity as well as temporal and spatial regulation of the interactions between p97 and its cofactors is only beginning to be understood at the molecular level. Here, we give an overview on the structural framework of p97 interactions with its cofactors, the emerging principles underlying the assembly of complexes with different cofactors, and the pathogenic effects of disease-associated p97 mutations on cofactor binding.
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78
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Zhang X, Gui L, Zhang X, Bulfer SL, Sanghez V, Wong DE, Lee Y, Lehmann L, Lee JS, Shih PY, Lin HJ, Iacovino M, Weihl CC, Arkin MR, Wang Y, Chou TF. Altered cofactor regulation with disease-associated p97/VCP mutations. Proc Natl Acad Sci U S A 2015; 112:E1705-14. [PMID: 25775548 PMCID: PMC4394316 DOI: 10.1073/pnas.1418820112] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dominant mutations in p97/VCP (valosin-containing protein) cause a rare multisystem degenerative disease with varied phenotypes that include inclusion body myopathy, Paget's disease of bone, frontotemporal dementia, and amyotrophic lateral sclerosis. p97 disease mutants have altered N-domain conformations, elevated ATPase activity, and altered cofactor association. We have now discovered a previously unidentified disease-relevant functional property of p97 by identifying how the cofactors p37 and p47 regulate p97 ATPase activity. We define p37 as, to our knowledge, the first known p97-activating cofactor, which enhances the catalytic efficiency (kcat/Km) of p97 by 11-fold. Whereas both p37 and p47 decrease the Km of ATP in p97, p37 increases the kcat of p97. In contrast, regulation by p47 is biphasic, with decreased kcat at low levels but increased kcat at higher levels. By deleting a region of p47 that lacks homology to p37 (amino acids 69-92), we changed p47 from an inhibitory cofactor to an activating cofactor, similar to p37. Our data suggest that cofactors regulate p97 ATPase activity by binding to the N domain. Induced conformation changes affect ADP/ATP binding at the D1 domain, which in turn controls ATPase cycling. Most importantly, we found that the D2 domain of disease mutants failed to be activated by p37 or p47. Our results show that cofactors play a critical role in controlling p97 ATPase activity, and suggest that lack of cofactor-regulated communication may contribute to p97-associated disease pathogenesis.
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Affiliation(s)
- Xiaoyi Zhang
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502; College of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Lin Gui
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502; College of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Xiaoyan Zhang
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048
| | - Stacie L Bulfer
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Valentina Sanghez
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - Daniel E Wong
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - YouJin Lee
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110
| | - Lynn Lehmann
- NanoTemper Technologies, Inc., South San Francisco, CA 94080
| | - James Siho Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Pei-Yin Shih
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Henry J Lin
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - Michelina Iacovino
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110
| | - Michelle R Arkin
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502;
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Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJS. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. ACTA ACUST UNITED AC 2015; 20:788-800. [PMID: 25690569 DOI: 10.1177/1087057115570550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/02/2015] [Indexed: 01/25/2023]
Abstract
The ubiquitous AAA+ ATPase p97 functions as a dynamic molecular machine driving several cellular processes. It is essential in regulating protein homeostasis, and it represents a potential drug target for cancer, particularly when there is a greater reliance on the endoplasmic reticulum-associated protein degradation pathway and ubiquitin-proteasome pathway to degrade an overabundance of secreted proteins. Here, we report a case study for using fragment-based ligand design approaches against this large and dynamic hexamer, which has multiple potential binding sites for small molecules. A screen of a fragment library was conducted by surface plasmon resonance (SPR) and followed up by nuclear magnetic resonance (NMR), two complementary biophysical techniques. Virtual screening was also carried out to examine possible binding sites for the experimental hits and evaluate the potential utility of fragment docking for this target. Out of this effort, 13 fragments were discovered that showed reversible binding with affinities between 140 µM and 1 mM, binding stoichiometries of 1:1 or 2:1, and good ligand efficiencies. Structural data for fragment-protein interactions were obtained with residue-specific [U-(2)H] (13)CH3-methyl-labeling NMR strategies, and these data were compared to poses from docking. The combination of virtual screening, SPR, and NMR enabled us to find and validate a number of interesting fragment hits and allowed us to gain an understanding of the structural nature of fragment binding.
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Affiliation(s)
- Michael S Chimenti
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - Stacie L Bulfer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Thomas L James
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
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80
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Weihl CC, Baloh RH, Lee Y, Chou TF, Pittman SK, Lopate G, Allred P, Jockel-Balsarotti J, Pestronk A, Harms MB. Targeted sequencing and identification of genetic variants in sporadic inclusion body myositis. Neuromuscul Disord 2015; 25:289-96. [PMID: 25617006 DOI: 10.1016/j.nmd.2014.12.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/15/2014] [Accepted: 12/28/2014] [Indexed: 12/14/2022]
Abstract
Sporadic inclusion body myositis (sIBM) has clinical, pathologic and pathomechanistic overlap with some inherited muscle and neurodegenerative disorders. In this study, DNA from 79 patients with sIBM was collected and the sequencing of 38 genes associated with hereditary inclusion body myopathy (IBM), myofibrillar myopathy, Emery-Dreifuss muscular dystrophy, distal myopathy, amyotrophic lateral sclerosis and dementia along with C9orf72 hexanucleotide repeat analysis was performed. No C9orf72 repeat expansions were identified, but; 27 rare (minor allele frequency <1%) missense coding variants in several other genes were identified. One patient carried a p.R95C missense mutation in VCP and another carried a previously reported p.I27V missense mutation in VCP. Mutations in VCP cause IBM associated with Paget's disease of the bone (PDB) and fronto-temporal dementia (IBMPFD). Neither patient had a family history of weakness or manifested other symptoms reported with VCP mutations such as PDB or dementia. In vitro analysis of these VCP variants found that they both disrupted autophagy similar to other pathogenic mutations. Although no clear genetic etiology has been implicated in sIBM pathogenesis, our study suggests that genetic evaluation in sIBM may be clinically meaningful and lend insight into its pathomechanism.
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Affiliation(s)
- Conrad C Weihl
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States.
| | - Robert H Baloh
- Department of Neurology, Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8730 Alden Drive, Los Angeles, CA 90048, United States
| | - Youjin Lee
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Centre, Los Angeles Biomedical Research Institute, Torrance, CA 90502, United States
| | - Sara K Pittman
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Glenn Lopate
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Peggy Allred
- Department of Neurology, Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8730 Alden Drive, Los Angeles, CA 90048, United States
| | - Jennifer Jockel-Balsarotti
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Alan Pestronk
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Matthew B Harms
- Department of Neurology, Hope Center for Neurologic Disorders, Washington University School of Medicine, Saint Louis, MO 63110, United States
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81
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Song C, Wang Q, Song C, Lockett SJ, Colburn NH, Li CCH, Wang JM, Rogers TJ. Nucleocytoplasmic shuttling of valosin-containing protein (VCP/p97) regulated by its N domain and C-terminal region. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1853:222-32. [PMID: 25447673 PMCID: PMC4254625 DOI: 10.1016/j.bbamcr.2014.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 10/01/2014] [Accepted: 10/21/2014] [Indexed: 12/25/2022]
Abstract
Valosin-containing protein (VCP or p97), a member of the AAA family (ATPases associated with diverse cellular activities), plays a key role in many important cellular activities. A genetic deficiency of VCP can cause inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia (IBMPFD). Previous studies showed that the VCP N domain is essential for the regulation of nuclear entry of VCP. Here we report that IBMPFD mutations, which are mainly located in the N domain, suppress the nuclear entry of VCP. Moreover, the peptide sequence G780AGPSQ in the C-terminal region regulates the retention of VCP in the nucleus. A mutant lacking this sequence can increase the nuclear distribution of IBMPFD VCP, suggesting that this sequence is a potential molecular target for correcting the deficient nucleocytoplasmic shuttling of IBMPFD VCP proteins.
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Affiliation(s)
- Changcheng Song
- Center for Inflammation, Translational and Clinical Lung Research, School of Medicine, Temple University, Philadelphia, PA 19140, USA.
| | - Qing Wang
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY, USA
| | - Changzheng Song
- Erythrocrine Project of Translational Medicine, Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Advanced Technology Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Nancy H Colburn
- Laboratory of Cancer Prevention, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chou-Chi H Li
- Laboratory of Cancer Prevention, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Basic Research Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Ji Ming Wang
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Thomas J Rogers
- Center for Inflammation, Translational and Clinical Lung Research, School of Medicine, Temple University, Philadelphia, PA 19140, USA
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82
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Chaturvedi L, Sun K, Walsh MF, Kuhn LA, Basson MD. The P-loop region of Schlafen 3 acts within the cytosol to induce differentiation of human Caco-2 intestinal epithelial cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:3029-37. [PMID: 25261706 DOI: 10.1016/j.bbamcr.2014.09.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/05/2014] [Accepted: 09/17/2014] [Indexed: 01/26/2023]
Abstract
Schlafen 3 (Slfn3) mediates rodent enterocyte differentiation in vitro and in vivo, required for intestinal function. Little is known about Schlafen protein structure-function relationships. To define the Slfn3 domain that promotes differentiation, we studied villin and sucrase isomaltase (SI) promoter activity in Slfn3-null human Caco-2BBE cells transfected with full-length rat Slfn3 DNA or truncated constructs. Confocal microscopy and Western blots showed that Slfn3 is predominantly cytosolic. Villin promoter activity, increased by wild type Slfn3, was further enhanced by adding a nuclear exclusion sequence, suggesting that Slfn3 does not affect transcription by direct nuclear action. We therefore sought to dissect the region in Slfn3 stimulating promoter activity. Since examination of the Slfn3 N-terminal region revealed sequences similar to both an aminopeptidase (App) and a divergent P-loop resembling those in NTPases, we initially divided Slfn3 into an N-terminal domain containing the App and P-loop regions, and a C-terminal region. Only the N-terminal construct stimulated promoter activity. Further truncation indicated that both the App and the smaller P-loop constructs enhanced promoter activity similarly to the N-terminal sequence. Point mutations within the N-terminal region (R128L, altering a critical active site residue in the App domain, and L212D, conserved in Schlafens but variable in P-loop proteins) did not affect activity. These results show that Slfn3 acts in the cytosol to trigger a secondary signal cascade that elicits differentiation marker expression and narrows the active domain to the third of the Slfn3 sequence homologous to P-loop NTPases, a first step in understanding its mechanism of action.
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Affiliation(s)
| | - Kelian Sun
- Department of Surgery, Michigan State University, East Lansing, MI, USA.
| | - Mary F Walsh
- Department of Surgery, Michigan State University, East Lansing, MI, USA.
| | - Leslie A Kuhn
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Computer Science & Engineering, Michigan State University, East Lansing, MI, USA.
| | - Marc D Basson
- Department of Surgery, Michigan State University, East Lansing, MI, USA.
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83
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Liang CJ, Chang YC, Chang HC, Wang CK, Hung YC, Lin YE, Chan CC, Chen CH, Chang HY, Sang TK. Derlin-1 regulates mutant VCP-linked pathogenesis and endoplasmic reticulum stress-induced apoptosis. PLoS Genet 2014; 10:e1004675. [PMID: 25255315 PMCID: PMC4177747 DOI: 10.1371/journal.pgen.1004675] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 08/14/2014] [Indexed: 12/13/2022] Open
Abstract
Mutations in VCP (Valosin-containing protein), an AAA ATPase critical for ER-associated degradation, are linked to IBMPFD (Inclusion body myopathy with Paget disease and frontotemporal dementia). Using a Drosophila IBMPFD model, we have identified the ER protein Derlin-1 as a modifier of pathogenic TER94 (the fly VCP homolog) mutants. Derlin-1 binds to TER94 directly, and this interaction is essential for Derlin-1 overexpression to suppress the pathogenic TER94-induced neurodegeneration. Derlin-1 overexpression reduces the elevated ATPase activity of pathogenic TER94, implying that IBMPFD is caused by ATPase hyper-activation. Under physiological condition, Derlin-1 expression is increased upon ER stress to recruit TER94 to the ER. However, in response to severe ER stress, Derlin-1 is required for activating apoptosis to eliminate damaged cells. This pro-apoptotic response is mimicked by Derlin-1 overexpression, which elicits acute ER stress and triggers apoptosis via a novel C-terminal motif (α). As this Derlin-1-dependent cell death is negated by TER94 overexpression, we propose that while Derlin-1 and VCP work cooperatively in ER stress response, their imbalance has a role in removing cells suffering prolonged ER stress. We have previously developed a fly model for IBMPFD (inclusion body myopathy with Paget disease and frontotemporal dementia) and demonstrated that specific mutations in VCP gene, a highly conserved ATPase, cause muscle and neuron degeneration by depleting cellular ATP level. Using this model, we show that expression of Derlin-1, an ER membrane protein capable of directly interacting with VCP, restores the normal cellular ATP level and suppresses IBMPFD-like neurodegeneration. As Derlin-1 expression can be induced by tunicamycin (an antibiotic) in experimental systems, our findings may yield new therapeutic strategies for VCP-linked diseases. In addition, we have obtained important insights regarding Derlin-1 function under physiological conditions. ER stress, caused by accumulation of improperly folded proteins, results in increased Derlin-1 expression, which is important for ER stress-induced cell death. We propose that Derlin-1 promotes ER homeostasis through multiple mechanisms. In addition to cooperating with VCP to extract improperly folded proteins from the ER, elevated Derlin-1 expression removes cells suffering from irreparable ER stress, thus preventing these damaged cells from further harming the organisms.
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Affiliation(s)
- Cyong-Jhih Liang
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ya-Chu Chang
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Henry C. Chang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Chung-Kang Wang
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Chien Hung
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ying-Er Lin
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Ching Chan
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chun-Hong Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Hui-Yun Chang
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - Tzu-Kang Sang
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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84
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Kang M, Wu T, Wijeratne EMK, Lau EC, Mason DJ, Mesa C, Tillotson J, Zhang DD, Gunatilaka AAL, La Clair JJ, Chapman E. Functional chromatography reveals three natural products that target the same protein with distinct mechanisms of action. Chembiochem 2014; 15:2125-31. [PMID: 25125376 PMCID: PMC4187115 DOI: 10.1002/cbic.201402258] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Indexed: 01/12/2023]
Abstract
Access to lead compounds with defined molecular targets continues to be a barrier to the translation of natural product resources. As a solution, we developed a system that uses discrete, recombinant proteins as the vehicles for natural product isolation. Here, we describe the use of this functional chromatographic method to identify natural products that bind to the AAA+ chaperone, p97, a promising cancer target. Application of this method to a panel of fungal and plant extracts identified rheoemodin, 1-hydroxydehydroherbarin, and phomapyrrolidone A as distinct p97 modulators. Excitingly, each of these molecules displayed a unique mechanism of p97 modulation. This discovery provides strong support for the application of functional chromatography to the discovery of protein modulators that would likely escape traditional high-throughput or phenotypic screening platforms.
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Affiliation(s)
- MinJin Kang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Tongde Wu
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - E. M. Kithsiri Wijeratne
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85706-6800, United States
| | - Eric C. Lau
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Damian J. Mason
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Celestina Mesa
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Joseph Tillotson
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - Donna D. Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85706-6800, United States
| | - James J. La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA 92163-1052, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, United States
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85
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Meyer H, Weihl CC. The VCP/p97 system at a glance: connecting cellular function to disease pathogenesis. J Cell Sci 2014; 127:3877-83. [PMID: 25146396 DOI: 10.1242/jcs.093831] [Citation(s) in RCA: 285] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ATPase valosin-containing protein (VCP)/p97 has emerged as a central and important element of the ubiquitin system. Together with a network of cofactors, it regulates an ever-expanding range of processes that stretch into almost every aspect of cellular physiology. Its main role in proteostasis and key functions in signaling pathways are of relevance to degenerative diseases and genomic stability. In this Cell Science at a Glance and the accompanying poster, we give a brief overview of this complex system. In addition, we discuss the pathogenic basis for VCP/p97-associated diseases and then highlight in more detail new exciting links to the translational stress response and RNA biology that further underscore the significance of the VCP/p97 system.
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Affiliation(s)
- Hemmo Meyer
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Conrad C Weihl
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO 63110, USA
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86
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Gonzalez MA, Feely SM, Speziani F, Strickland AV, Danzi M, Bacon C, Lee Y, Chou TF, Blanton SH, Weihl CC, Zuchner S, Shy ME. A novel mutation in VCP causes Charcot-Marie-Tooth Type 2 disease. ACTA ACUST UNITED AC 2014; 137:2897-902. [PMID: 25125609 DOI: 10.1093/brain/awu224] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Mutations in VCP have been reported to account for a spectrum of phenotypes that include inclusion body myopathy with Paget's disease of the bone and frontotemporal dementia, hereditary spastic paraplegia, and 1-2% of familial amyotrophic lateral sclerosis. We identified a novel VCP mutation (p.Glu185Lys) segregating in an autosomal dominant Charcot-Marie-Tooth disease type 2 family. Functional studies showed that the Glu185Lys variant impaired autophagic function leading to the accumulation of immature autophagosomes. VCP mutations should thus be considered for genetically undefined Charcot-Marie-Tooth disease type 2.
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Affiliation(s)
- Michael A Gonzalez
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Shawna M Feely
- 2 Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Fiorella Speziani
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alleene V Strickland
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Matt Danzi
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Chelsea Bacon
- 2 Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Youjin Lee
- 3 Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Tsui-Fen Chou
- 4 Division of Medical Genetics, Department of Paediatrics, Harbor-UCLA Medical Centre and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA
| | - Susan H Blanton
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Conrad C Weihl
- 3 Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Stephan Zuchner
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Michael E Shy
- 2 Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
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87
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Chou TF, Bulfer SL, Weihl CC, Li K, Lis LG, Walters MA, Schoenen FJ, Lin HJ, Deshaies RJ, Arkin MR. Specific inhibition of p97/VCP ATPase and kinetic analysis demonstrate interaction between D1 and D2 ATPase domains. J Mol Biol 2014; 426:2886-99. [PMID: 24878061 PMCID: PMC4102644 DOI: 10.1016/j.jmb.2014.05.022] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
The p97 AAA (ATPase associated with diverse cellular activities), also called VCP (valosin-containing protein), is an important therapeutic target for cancer and neurodegenerative diseases. p97 forms a hexamer composed of two AAA domains (D1 and D2) that form two stacked rings and an N-terminal domain that binds numerous cofactor proteins. The interplay between the three domains in p97 is complex, and a deeper biochemical understanding is needed in order to design selective p97 inhibitors as therapeutic agents. It is clear that the D2 ATPase domain hydrolyzes ATP in vitro, but whether D1 contributes to ATPase activity is controversial. Here, we use Walker A and B mutants to demonstrate that D1 is capable of hydrolyzing ATP and show for the first time that nucleotide binding in the D2 domain increases the catalytic efficiency (kcat/Km) of D1 ATP hydrolysis 280-fold, by increasing kcat 7-fold and decreasing Km about 40-fold. We further show that an ND1 construct lacking D2 but including the linker between D1 and D2 is catalytically active, resolving a conflict in the literature. Applying enzymatic observations to small-molecule inhibitors, we show that four p97 inhibitors (DBeQ, ML240, ML241, and NMS-873) have differential responses to Walker A and B mutations, to disease-causing IBMPFD mutations, and to the presence of the N domain binding cofactor protein p47. These differential effects provide the first evidence that p97 cofactors and disease mutations can alter p97 inhibitor potency and suggest the possibility of developing context-dependent inhibitors of p97.
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Affiliation(s)
- Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA.
| | - Stacie L Bulfer
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelin Li
- Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
| | - Lev G Lis
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Frank J Schoenen
- Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
| | - Henry J Lin
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA
| | - Raymond J Deshaies
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA
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88
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Architecture and assembly of the archaeal Cdc48*20S proteasome. Proc Natl Acad Sci U S A 2014; 111:E1687-94. [PMID: 24711419 DOI: 10.1073/pnas.1404823111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
ATP-dependent proteases maintain protein quality control and regulate diverse intracellular functions. Proteasomes are primarily responsible for these tasks in the archaeal and eukaryotic domains of life. Even the simplest of these proteases function as large complexes, consisting of the 20S peptidase, a barrel-like structure composed of four heptameric rings, and one or two AAA+ (ATPase associated with a variety of cellular activities) ring hexamers, which use cycles of ATP binding and hydrolysis to unfold and translocate substrates into the 20S proteolytic chamber. Understanding how the AAA+ and 20S components of these enzymes interact and collaborate to execute protein degradation is important, but the highly dynamic nature of prokaryotic proteasomes has hampered structural characterization. Here, we use electron microscopy to determine the architecture of an archaeal Cdc48 ⋅ 20S proteasome, which we stabilized by site-specific cross-linking. This complex displays coaxial alignment of Cdc48 and 20S and is enzymatically active, demonstrating that AAA+ unfoldase wobbling with respect to 20S is not required for function. In the complex, the N-terminal domain of Cdc48, which regulates ATP hydrolysis and degradation, packs against the D1 ring of Cdc48 in a coplanar fashion, constraining mechanisms by which the N-terminal domain alters 20S affinity and degradation activity.
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89
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Yeung HO, Förster A, Bebeacua C, Niwa H, Ewens C, McKeown C, Zhang X, Freemont PS. Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy. Open Biol 2014; 4:130142. [PMID: 24598262 PMCID: PMC3971404 DOI: 10.1098/rsob.130142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes.
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Affiliation(s)
- Heidi O Yeung
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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90
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Tang WK, Xia D. Altered intersubunit communication is the molecular basis for functional defects of pathogenic p97 mutants. J Biol Chem 2013; 288:36624-35. [PMID: 24196964 DOI: 10.1074/jbc.m113.488924] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The human AAA ATPase p97 is a molecular chaperone essential in cellular proteostasis. Single amino acid substitutions in p97 have been linked to a clinical multiple-disorder condition known as inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia. How the mutations affect the molecular mechanism that governs the function of p97 remains unclear. Here, we show that within the hexameric ring of a mutant p97, D1 domains fail to regulate their respective nucleotide-binding states, as evidenced by the lower amount of prebound ADP, weaker ADP binding affinity, full occupancy of adenosine-5'-O-(3-thiotriphosphate) binding, and elevated overall ATPase activity, indicating a loss of communication among subunits. Defective communication between subunits is further illustrated by altered conformation in the side chain of residue Phe-360 that probes into the nucleotide-binding pocket from a neighboring subunit. Consequently, conformations of N domains in a hexameric ring of a mutant p97 become uncoordinated, thus impacting its ability to process substrate.
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Affiliation(s)
- Wai Kwan Tang
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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91
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Cdc48: a swiss army knife of cell biology. JOURNAL OF AMINO ACIDS 2013; 2013:183421. [PMID: 24167726 PMCID: PMC3791797 DOI: 10.1155/2013/183421] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/29/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.
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92
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Saibil H. Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 2013; 14:630-42. [PMID: 24026055 DOI: 10.1038/nrm3658] [Citation(s) in RCA: 706] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular chaperones are diverse families of multidomain proteins that have evolved to assist nascent proteins to reach their native fold, protect subunits from heat shock during the assembly of complexes, prevent protein aggregation or mediate targeted unfolding and disassembly. Their increased expression in response to stress is a key factor in the health of the cell and longevity of an organism. Unlike enzymes with their precise and finely tuned active sites, chaperones are heavy-duty molecular machines that operate on a wide range of substrates. The structural basis of their mechanism of action is being unravelled (in particular for the heat shock proteins HSP60, HSP70, HSP90 and HSP100) and typically involves massive displacements of 20-30 kDa domains over distances of 20-50 Å and rotations of up to 100°.
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Affiliation(s)
- Helen Saibil
- Department of Crystallography, Institute for Structural and Molecular Biology, Birkbeck College London, UK
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93
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Suvorova ES, Radke JB, Ting LM, Vinayak S, Alvarez CA, Kratzer S, Kim K, Striepen B, White MW. A nucleolar AAA-NTPase is required for parasite division. Mol Microbiol 2013; 90:338-55. [PMID: 23964771 DOI: 10.1111/mmi.12367] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2013] [Indexed: 01/02/2023]
Abstract
Apicomplexa division involves several distinct phases shared with other eukaryote cell cycles including a gap period (G1) prior to chromosome synthesis, although how progression through the parasite cell cycle is controlled is not understood. Here we describe a cell cycle mutant that reversibly arrests in the G1 phase. The defect in this mutant was mapped by genetic complementation to a gene encoding a novel AAA-ATPase/CDC48 family member called TgNoAP1. TgNoAP1 is tightly regulated and expressed in the nucleolus during the G1/S phases. A tyrosine to a cysteine change upstream of the second AAA+ domain in the temperature sensitive TgNoAP1 allele leads to conditional protein instability, which is responsible for rapid cell cycle arrest and a primary defect in 28S rRNA processing as confirmed by knock-in of the mutation back into the parent genome. The interaction of TgNoAP1 with factors of the snoRNP and R2TP complexes indicates this protein has a role in pre-rRNA processing. This is a novel role for a cdc48-related chaperone protein and indicates that TgNoAP1 may be part of a dynamic mechanism that senses the health of the parasite protein machinery at the initial steps of ribosome biogenesis and conveys that information to the parasite cell cycle checkpoint controls.
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Affiliation(s)
- Elena S Suvorova
- Departments of Molecular Medicine & Global Health, University of South Florida, Tampa, FL, 33612, USA
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94
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Liu CC, Sun S, Sui SF. The role of the N-D1 linker of the N-ethylmaleimide-sensitive factor in the SNARE disassembly. PLoS One 2013; 8:e64346. [PMID: 23667709 PMCID: PMC3646813 DOI: 10.1371/journal.pone.0064346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/10/2013] [Indexed: 12/04/2022] Open
Abstract
N-ethylmaleimide-sensitive factor (NSF) is a member of the type II AAA+ (ATPase associated with various cellular activities) family. It plays a critical role in intracellular membrane trafficking by disassembling soluble NSF attachment protein receptor (SNARE) complexes. Each NSF protomer consists of an N-terminal domain (N domain) followed by two AAA ATPase domains (D1 and D2) in tandem. The N domain is required for SNARE/α-SNAP binding and the D1 domain accounts for the majority of ATP hydrolysis. Little is known about the role of the N-D1 linker in the NSF function. This study presents detailed mutagenesis analyses of NSF N-D1 linker, dissecting its role in the SNARE disassembly, the SNARE/α-SNAP complex binding, the basal ATPase activity and the SNARE/α-SNAP stimulated ATPase activity. Our results show that the N-terminal region of the N-D1 linker associated mutants cause severe defect in SNARE complex disassembly, but little effects on the SNARE/α-SNAP complex binding, the basal and the SNARE/α-SNAP stimulated ATPase activity, suggesting this region may be involved in the motion transmission from D1 to N domain. Mutating the residues in middle and C-terminal region of the N-D1 linker increases the basal ATPase activity, indicating it may play a role in autoinhibiting NSF activity until it encounters SNARE/α-SNAP complex substrate. Moreover, mutations at the C-terminal sequence GIGG exhibit completely abolished or severely reduced activities of the substrate binding, suggesting that the flexibility of N-D1 linker is critical for the movement of the N domain that is required for the substrate binding. Taken together, these data suggest that the whole N-D1 linker is critical for the biological function of NSF to disassemble SNARE complex substrate with different regions responsible for different roles.
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Affiliation(s)
- Cui-Cui Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail: (SS); (SFS)
| | - Sen-Fang Sui
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail: (SS); (SFS)
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95
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Mehta SG, Khare M, Ramani R, Watts GDJ, Simon M, Osann KE, Donkervoort S, Dec E, Nalbandian A, Platt J, Pasquali M, Wang A, Mozaffar T, Smith CD, Kimonis VE. Genotype-phenotype studies of VCP-associated inclusion body myopathy with Paget disease of bone and/or frontotemporal dementia. Clin Genet 2013; 83:422-31. [PMID: 22909335 PMCID: PMC3618576 DOI: 10.1111/cge.12000] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/16/2012] [Accepted: 08/16/2012] [Indexed: 12/12/2022]
Abstract
Valosin containing protein (VCP) disease associated with inclusion body myopathy, Paget disease of the bone and frontotemporal dementia is a progressive autosomal dominant disorder caused by mutations in Valosin containing protein gene. To establish genotype-phenotype correlations we analyzed clinical and biochemical markers from a database of 190 members in 27 families harboring 10 missense mutations. Individuals were grouped into three categories: symptomatic, presymptomatic carriers and noncarriers. The symptomatic families were further divided into ten groups based on their VCP mutations. There was marked intra and inter-familial variation; and significant genotype-phenotype correlations were difficult to establish because of small numbers. Nevertheless when comparing the two most common mutations, R155C mutation was found to be more severe, with an earlier onset of myopathy and Paget (p = 0.03). Survival analysis of all subjects revealed an average life span after diagnosis of myopathy and Paget of 18 and 19 years respectively, and after dementia only 6 years. R155C had a reduced survival compared to the R155H mutation (p = 0.03).We identified amyotrophic lateral sclerosis (ALS) was diagnosed in 13 individuals (8.9%) and Parkinson's disease in five individuals (3%); however, there was no genotypic correlation. This study represents the largest dataset of patients with VCP disease and expands our understanding of the natural history and provides genotype-phenotype correlations in this unique disease.
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Affiliation(s)
- Sarju G. Mehta
- East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, UK
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
| | - Manaswitha Khare
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
| | - Rupal Ramani
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
| | - Giles D. J. Watts
- Biomedical Research Center, University of East Anglia, Norwich, Norfolk
| | - Mariella Simon
- Mitomed Laboratory, University of California, Irvine, CA
| | - Kathryn E. Osann
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA
| | - Sandra Donkervoort
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
| | - Eric Dec
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
| | - Angele Nalbandian
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
| | - Julia Platt
- Mitomed Laboratory, University of California, Irvine, CA
| | - Marzia Pasquali
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT
| | - Annabel Wang
- ALS and Neuromuscular Center, University of California, Irvine, CA
| | - Tahseen Mozaffar
- ALS and Neuromuscular Center, University of California, Irvine, CA
| | - Charles D. Smith
- Department of Neurology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Virginia E. Kimonis
- Division of Genetics and Metabolism, Department of Pediatrics, University of California, Irvine, CA
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96
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Chia WS, Chia DX, Rao F, Bar Nun S, Geifman Shochat S. ATP binding to p97/VCP D1 domain regulates selective recruitment of adaptors to its proximal N-domain. PLoS One 2012; 7:e50490. [PMID: 23226521 PMCID: PMC3513293 DOI: 10.1371/journal.pone.0050490] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 10/23/2012] [Indexed: 11/18/2022] Open
Abstract
p97/Valosin-containing protein (VCP) is a member of the AAA-ATPase family involved in many cellular processes including cell division, intracellular trafficking and extraction of misfolded proteins in endoplasmic reticulum-associated degradation (ERAD). It is a homohexamer with each subunit containing two tandem D1 and D2 ATPase domains and N- and C-terminal regions that function as adaptor protein binding domains. p97/VCP is directed to its many different functional pathways by associating with various adaptor proteins. The regulation of the recruitment of the adaptor proteins remains unclear. Two adaptor proteins, Ufd1/Npl4 and p47, which bind exclusively to the p97/VCP N-domain and direct p97/VCP to either ERAD-related processes or homotypic fusion of Golgi fragments, were studied here. Surface plasmon resonance biosensor-based assays allowed the study of binding kinetics in real time. In competition experiments, it was observed that in the presence of ATP, Ufd1/Npl4 was able to compete more effectively with p47 for binding to p97/VCP. By using non-hydrolysable ATP analogues and the hexameric truncated p97/N-D1 fragment, it was shown that binding rather than hydrolysis of ATP to the proximal D1 domain strengthened the Ufd1/Npl4 association with the N-domain, thus regulating the recruitment of either Ufd1/Npl4 or p47. This novel role of ATP and an assigned function to the D1 AAA-ATPase domain link the multiple functions of p97/VCP to the metabolic status of the cell.
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Affiliation(s)
- Wei Sheng Chia
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Diana Xueqi Chia
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Feng Rao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shoshana Bar Nun
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Susana Geifman Shochat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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97
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Barthelme D, Sauer RT. Identification of the Cdc48•20S proteasome as an ancient AAA+ proteolytic machine. Science 2012; 337:843-6. [PMID: 22837385 DOI: 10.1126/science.1224352] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Proteasomes are the major energy-dependent proteolytic machines in the eukaryotic and archaeal domains of life. To execute protein degradation, the 20S core peptidase combines with the AAA+ ring of the 19S regulatory particle in eukarya or with the AAA+ proteasome-activating nucleotidase ring in some archaea. Here, we find that Cdc48 and 20S from the archaeon Thermoplasma acidophilum interact to form a functional proteasome. Cdc48 is an abundant and essential double-ring AAA+ molecular machine ubiquitously present in archaea, where its function has been uncertain, and in eukarya where Cdc48 participates by largely unknown mechanisms in diverse cellular processes, including multiple proteolytic pathways. Thus, proteolysis in collaboration with the 20S peptidase may represent an ancestral function of the Cdc48 family.
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Affiliation(s)
- Dominik Barthelme
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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98
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Tang WK, Xia D. Structural and functional deviations in disease-associated p97 mutants. J Struct Biol 2012; 179:83-92. [PMID: 22579784 DOI: 10.1016/j.jsb.2012.04.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/23/2012] [Accepted: 04/28/2012] [Indexed: 11/28/2022]
Abstract
Missense mutations that occur at the interface between two functional domains in the AAA protein p97 lead to suboptimal performance in its enzymatic activity and impaired intracellular functions, causing human disorders such as inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). Much progress has been made in characterizing these mutants at cellular, sub-cellular and molecular levels, gaining a substantial understanding of the involvement of p97 in various cellular pathways. At the tissue level, patient biopsies revealed co-localization of p97 with pathologic proteineous inclusions and rimmed vacuoles, which can be reproduced in various cellular and animal models of IBMPFD. At the subcellular level, alterations in p97's ability to bind various adaptor proteins have been demonstrated for some but not all binding partners. Biochemical and biophysical characterizations of pathogenic p97 revealed altered nucleotide binding properties in the D1-domains compared to the wild type. Structural studies showed that mutant p97 are capable of undergoing a uniform transition in the N-domain from a Down- to an Up-conformation in the presence of ATPγS, while in the wild-type p97, this conformational change can only be demonstrated in solutions but not in crystals. These structural and biochemical analyses of IBMPFD mutants shed new light into the mechanism of p97 function.
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Affiliation(s)
- Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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