201
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Li DHS, Chung YS, Gloyd M, Joseph E, Ghirlando R, Wright GD, Cheng YQ, Maurizi MR, Guarné A, Ortega J. Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP. CHEMISTRY & BIOLOGY 2010; 17:959-69. [PMID: 20851345 PMCID: PMC2955292 DOI: 10.1016/j.chembiol.2010.07.008] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/06/2010] [Accepted: 07/08/2010] [Indexed: 01/07/2023]
Abstract
In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli ClpP bound to ADEP1 and report the structural changes underlying ClpP activation. ADEP1 binds in the hydrophobic groove that serves as the primary docking site for ClpP ATPases. Binding of ADEP1 locks the N-terminal loops of ClpP in a β-hairpin conformation, generating a stable pore through which extended polypeptides can be threaded. This structure serves as a model for ClpP in the holoenzyme ClpAP and ClpXP complexes and provides critical information to further develop this class of antibiotics.
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Affiliation(s)
- Dominic Him Shun Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
- MG. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Yu Seon Chung
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Melanie Gloyd
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Ebenezer Joseph
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0540, USA
| | - Gerard D. Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
- MG. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Yi-Qiang Cheng
- Department of Biological Sciences and Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
| | - Michael R. Maurizi
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
- MG. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, L8N3Z5, Canada
- Correspondence: Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, Room 4H24, McMaster University, 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada. Phone: 1-905-525-9140 Ext 22703 Fax: 1-905-522-9033.
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202
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Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. EMBO J 2010; 29:3520-30. [PMID: 20834233 DOI: 10.1038/emboj.2010.226] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 08/19/2010] [Indexed: 11/08/2022] Open
Abstract
Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress. Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad. We report the 2.0-Å resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible through an axial channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing the membrane anchor to form an apical domain that serves as a gate governing substrate access to an internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites without further gating restrictions.
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203
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Davies BA, Azmi IF, Payne J, Shestakova A, Horazdovsky BF, Babst M, Katzmann DJ. Coordination of substrate binding and ATP hydrolysis in Vps4-mediated ESCRT-III disassembly. Mol Biol Cell 2010; 21:3396-408. [PMID: 20702581 PMCID: PMC2947475 DOI: 10.1091/mbc.e10-06-0512] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Vps4 disassembly of ESCRT-III plays an important role in MVB sorting, viral budding, and cytokinesis. An in vitro system was developed to investigate this process. These studies revealed new insights into the mechanisms of Vps4 function. ESCRT-III undergoes dynamic assembly and disassembly to facilitate membrane exvagination processes including multivesicular body (MVB) formation, enveloped virus budding, and membrane abscission during cytokinesis. The AAA-ATPase Vps4 is required for ESCRT-III disassembly, however the coordination of Vps4 ATP hydrolysis with ESCRT-III binding and disassembly is not understood. Vps4 ATP hydrolysis has been proposed to execute ESCRT-III disassembly as either a stable oligomer or an unstable oligomer whose dissociation drives ESCRT-III disassembly. An in vitro ESCRT-III disassembly assay was developed to analyze Vps4 function during this process. The studies presented here support a model in which Vps4 acts as a stable oligomer during ATP hydrolysis and ESCRT-III disassembly. Moreover, Vps4 oligomer binding to ESCRT-III induces coordination of ATP hydrolysis at the level of individual Vps4 subunits. These results suggest that Vps4 functions as a stable oligomer that acts upon individual ESCRT-III subunits to facilitate ESCRT-III disassembly.
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Affiliation(s)
- Brian A Davies
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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204
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Gymnastics of Molecular Chaperones. Mol Cell 2010; 39:321-31. [DOI: 10.1016/j.molcel.2010.07.012] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 06/14/2010] [Accepted: 07/09/2010] [Indexed: 11/20/2022]
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205
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Ordering an engagement ring. Mol Cell 2010; 38:319-20. [PMID: 20471937 DOI: 10.1016/j.molcel.2010.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this issue of Molecular Cell, Tomko et al. (2010) establish that the six distinct ATPase subunits of the eukaryotic proteasome form a heterohexameric ring and resolve how the subunits are arranged within the ring.
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206
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Misic AM, Satyshur KA, Forest KT. P. aeruginosa PilT structures with and without nucleotide reveal a dynamic type IV pilus retraction motor. J Mol Biol 2010; 400:1011-21. [PMID: 20595000 DOI: 10.1016/j.jmb.2010.05.066] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 05/21/2010] [Accepted: 05/26/2010] [Indexed: 11/19/2022]
Abstract
Type IV pili are bacterial extracellular filaments that can be retracted to create force and motility. Retraction is accomplished by the motor protein PilT. Crystal structures of Pseudomonas aeruginosa PilT with and without bound beta,gamma-methyleneadenosine-5'-triphosphate have been solved at 2.6 A and 3.1 A resolution, respectively, revealing an interlocking hexamer formed by the action of a crystallographic 2-fold symmetry operator on three subunits in the asymmetric unit and held together by extensive ionic interactions. The roles of two invariant carboxylates, Asp Box motif Glu163 and Walker B motif Glu204, have been assigned to Mg(2+) binding and catalysis, respectively. The nucleotide ligands in each of the subunits in the asymmetric unit of the beta,gamma-methyleneadenosine-5'-triphosphate-bound PilT are not equally well ordered. Similarly, the three subunits in the asymmetric unit of both structures exhibit differing relative conformations of the two domains. The 12 degrees and 20 degrees domain rotations indicate motions that occur during the ATP-coupled mechanism of the disassembly of pili into membrane-localized pilin monomers. Integrating these observations, we propose a three-state "Ready, Active, Release" model for the action of PilT.
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Affiliation(s)
- Ana M Misic
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, 1550 Linden Drive, Madison, WI 53706, USA
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207
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Crozat E, Meglio A, Allemand JF, Chivers CE, Howarth M, Vénien-Bryan C, Grainge I, Sherratt DJ. Separating speed and ability to displace roadblocks during DNA translocation by FtsK. EMBO J 2010; 29:1423-33. [PMID: 20379135 PMCID: PMC2868570 DOI: 10.1038/emboj.2010.29] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/12/2010] [Indexed: 11/18/2022] Open
Abstract
FtsK translocates dsDNA directionally at >5 kb/s, even under strong forces. In vivo, the action of FtsK at the bacterial division septum is required to complete the final stages of chromosome unlinking and segregation. Despite the availability of translocase structures, the mechanism by which ATP hydrolysis is coupled to DNA translocation is not understood. Here, we use covalently linked translocase subunits to gain insight into the DNA translocation mechanism. Covalent trimers of wild-type subunits dimerized efficiently to form hexamers with high translocation activity and an ability to activate XerCD-dif chromosome unlinking. Covalent trimers with a catalytic mutation in the central subunit formed hexamers with two mutated subunits that had robust ATPase activity. They showed wild-type translocation velocity in single-molecule experiments, activated translocation-dependent chromosome unlinking, but had an impaired ability to displace either a triplex oligonucleotide, or streptavidin linked to biotin-DNA, during translocation along DNA. This separation of translocation velocity and ability to displace roadblocks is more consistent with a sequential escort mechanism than stochastic, hand-off, or concerted mechanisms.
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Affiliation(s)
- Estelle Crozat
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Adrien Meglio
- Laboratoire de Physique Statistique et Département de Biologie, Ecole Normale Supérieure, UPMC, Paris 06, Université Paris Diderot, CNRS, Paris, France
| | - Jean-François Allemand
- Laboratoire de Physique Statistique et Département de Biologie, Ecole Normale Supérieure, UPMC, Paris 06, Université Paris Diderot, CNRS, Paris, France
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Ian Grainge
- Department of Biochemistry, University of Oxford, Oxford, UK
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208
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del Castillo U, Fernández-Higuero JA, Pérez-Acebrón S, Moro F, Muga A. Nucleotide utilization requirements that render ClpB active as a chaperone. FEBS Lett 2010; 584:929-34. [PMID: 20085762 DOI: 10.1016/j.febslet.2010.01.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 12/28/2009] [Accepted: 01/12/2010] [Indexed: 11/26/2022]
Abstract
ClpB is a member of the AAA+ superfamily that forms a ring-shaped homohexamer. Each protomer contains two nucleotide binding domains arranged in two rings that hydrolyze ATP. We extend here previous studies on ClpB nucleotide utilization requirements by using an experimental approach that maximizes random incorporation of different subunits into the protein hexamer. Incorporation of one subunit unable to bind or hydrolyze ATP knocks down the chaperone activity, while the wt hexamer can accommodate two mutant subunits that hydrolyze ATP in only one protein ring. Four subunits seem to build the functional cooperative unit, provided that one of the protein rings contains active nucleotide binding sites.
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Affiliation(s)
- Urko del Castillo
- Unidad de Biofísica (CSIC-UPV/EHU), and Departamento de Bioquímica y BiologíaMolecular (UPV/EHU), Facultad de Ciencia y Tecnología, Universidad del País Vasco, P.O. Box 644, Bilbao, Spain
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209
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Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease. Proc Natl Acad Sci U S A 2009; 106:19340-5. [PMID: 19892734 DOI: 10.1073/pnas.0910484106] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ClpXP is an ATP-fueled molecular machine that unfolds and degrades target proteins. ClpX, an AAA+ enzyme, recognizes specific proteins, and then uses cycles of ATP hydrolysis to denature any native structure and to translocate the unfolded polypeptide into ClpP for degradation. Here, we develop and apply single-molecule fluorescence assays to probe the kinetics of protein denaturation and degradation by ClpXP. These assays employ a single-chain variant of the ClpX hexamer, linked via a single biotin to a streptavidin-coated surface, and fusion substrates with an N-terminal fluorophore and a C-terminal GFP-titin-ssrA module. In the presence of adenosine 5'-[gamma-thio]triphosphate (ATPgammaS), ClpXP degrades the titin-ssrA portion of these substrates but stalls when it encounters GFP. Exchange into ATP then allows synchronous resumption of denaturation and degradation of GFP and any downstream domains. GFP unfolding can be monitored directly, because intrinsic fluorescence is quenched by denaturation. The time required for complete degradation coincides with loss of the substrate fluorophore from the protease complex. Fitting single-molecule data for a set of related substrates provides time constants for ClpX unfolding, translocation, and a terminal step that may involve product release. Comparison of these single-molecule results with kinetics measured in bulk solution indicates similar levels of microscopic and macroscopic ClpXP activity. These results support a stochastic engagement/unfolding mechanism that ultimately results in highly processive degradation and set the stage for more detailed single-molecule studies of machine function.
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