Crystal Structure of the ATPase Domain of the Human AAA+ Protein Paraplegin/SPG7
Publication Date
October 20, 2009
Journal
PLOS ONE
Authors
Tobias Karlberg, Susanne Van Den Berg, Martin Hammarström, Johanna Sagemark, et al
Volume
4
Issue
10
Pages
e6975
DOI
https://dx.plos.org/10.1371/journal.pone.0006975
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0006975
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19841671
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734466
Europe PMC
http://europepmc.org/abstract/MED/19841671
Web of Science
000271012900001
Scopus
70449411716
Mendeley
http://www.mendeley.com/research/crystal-structure-atpase-domain-human-aaa-protein-parapleginspg7
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Mendeley | Further Information

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Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/878902"], "description"=>"<p>Details of side chain interactions with ADP.</p>", "links"=>[], "tags"=>["nucleotide", "binding"], "article_id"=>549353, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006975.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_nucleotide_binding_site_of_paraplegin_/549353", "title"=>"The nucleotide binding site of paraplegin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-20 02:35:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/878703"], "description"=>"<p>A. Coomassie-stained SDS-polyacrylamide gel showing the purity of crude paraplegin<sup>305–565</sup> after TEV-cleavage (left lane; red asterisk, hexahistidine-tagged protein; black asterisk, cleaved protein), and after the final purification step (right lane). B. Example of crystals grown under the conditions that yielded diffraction data.</p>", "links"=>[], "tags"=>["crystallization"], "article_id"=>549160, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006975.g002", "stats"=>{"downloads"=>7, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Purification_and_crystallization_of_paraplegin_305_8211_565_/549160", "title"=>"Purification and crystallization of paraplegin<sup>305–565</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-20 02:32:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/879072"], "description"=>"<p>Values for the highest resolution shell are shown in parentheses.</p>†<p>R<sub>work</sub> is defined as Σ||F<sub>obs</sub>|−|F<sub>calc</sub>||/Σ |F<sub>obs</sub>|, where F<sub>obs</sub> and F<sub>calc</sub> are observed and calculated structure-factor amplitudes, respectively.</p>‡<p>R<sub>free</sub> is the R factor for the test set (5–10% of the data).</p>", "links"=>[], "tags"=>["refinement"], "article_id"=>549527, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006975.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Paraplegin_crystal_structure_Data_collection_and_refinement_statistics_/549527", "title"=>"Paraplegin crystal structure: Data collection and refinement statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-10-20 02:38:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/878558"], "description"=>"<p>A. Domain arrangement of paraplegin, FtsH, VCP, and spastin. Homologies included are the FtsH extracellular (Pfam entry PF36480), AAA+ (PF00004), metallopeptidase M41 (PF01434), Cell division protein-48 (CDC48) N-terminal (PF02359), CDC48-2 (PF02933), and microtubule interacting and transport (MIT; PF04212) domains. B. Sequence alignment of the ATPase domains of paraplegin and related proteins to illustrate the positions of conserved residues. Residue numbering and secondary structural elements are indicated for paraplegin (PDB entry 2qz4) above the alignment. Walker A and B, and Sensor 1 and 2 motifs, the arginine residue predicted to act as an arginine finger, as well as the pore loop are indicated below the alignment. Indicated by green asterisks are HSP disease related positions. Sequences shown are human paraplegin/SPG7 (residues 305–565; PDB entry 2qz4; gene identification code 116242796). <i>Thermus thermophilus</i> FtsH (126–624; 2dhr; gi:8051696), <i>Thermotoga maritima</i> FtsH (147–610; 2cea; gi:15643346), human p97/VCP (116–417; gi:112818458), and human spastin/SPG4 (114–437; gi:11875211).</p>", "links"=>[], "tags"=>["biochemistry/macromolecular assemblies and machines", "biochemistry/protein folding", "biochemistry/structural genomics", "genetics and genomics/genetics of disease"], "article_id"=>549007, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006975.g001", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Domain_arrangement_and_sequence_comparison_of_paraplegin_SPG7_and_related_AAA_proteins_/549007", "title"=>"Domain arrangement and sequence comparison of paraplegin/SPG7 and related AAA+ proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-20 02:30:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/878990"], "description"=>"<p>A. The hexameric structure of paraplegin<sup>305–565</sup> was modelled by aligning our crystal structure (blue) with each monomer within the <i>T. thermophilus</i> FtsH hexamer crystal structure (2dhr; orange). The outline of one monomer is indicated by grey shading, and the N- and C-termini of another monomer are indicated. The boxed area is expanded in panel B. B. Close-up of the region around the pore loops and the monomer interface around the nucleotide binding site. The hydrophobic pore loop residue Phe228 of FtsH, implicated in substrate binding, is shown in green, and the corresponding paraplegin residue Ile832 is shown in purple. Paraplegin Arg470, shown in red, is a putative arginine finger that activates ATP hydrolysis in the neighbor monomer following a conformational change in the ring structure.</p>", "links"=>[], "tags"=>["paraplegin"], "article_id"=>549448, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006975.g005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_of_the_paraplegin_hexamer_/549448", "title"=>"Model of the paraplegin hexamer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-20 02:37:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/436584", "https://ndownloader.figshare.com/files/436622"], "description"=>"<div><h3></h3><p>Paraplegin is an <em>m</em>-AAA protease of the mitochondrial inner membrane that is linked to hereditary spastic paraplegias. The gene encodes an FtsH-homology protease domain in tandem with an AAA+ homology ATPase domain. The protein is believed to form a hexamer that uses ATPase-driven conformational changes in its AAA-domain to deliver substrate peptides to its protease domain. We present the crystal structure of the AAA-domain of human paraplegin bound to ADP at 2.2 Å. This enables assignment of the roles of specific side chains within the catalytic cycle, and provides the structural basis for understanding the mechanism of disease mutations.</p><h3>Enhanced version</h3><p><b>This article can also be viewed as an <a href=\"http://plosone.org/enhanced/pone.0006975/\">enhanced version</a> in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006975#pone.0006975.s002\">Text S1</a>.</b></p></div>", "links"=>[], "tags"=>["atpase"], "article_id"=>146090, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0006975.s001", "https://dx.doi.org/10.1371/journal.pone.0006975.s002"], "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Crystal_Structure_of_the_ATPase_Domain_of_the_Human_AAA_Protein_Paraplegin_SPG7/146090", "title"=>"Crystal Structure of the ATPase Domain of the Human AAA+ Protein Paraplegin/SPG7", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-10-20 01:41:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/878781"], "description"=>"<p>A. Schematic representation of the crystal structure of a monomer of paraplegin<sup>305–565</sup> with bound ADP. Sequence motifs indicated in the sequence alignment in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006975#pone-0006975-g001\" target=\"_blank\">Figure 1</a> have been mapped onto the structure. The positions of disease-related residues are labeled in blue. B. Electrostatic surface representation of paraplegin<sup>305–565</sup> illustrating the nucleotide binding cleft.</p>", "links"=>[], "tags"=>["paraplegin", "atpase"], "article_id"=>549239, "categories"=>["Biochemistry", "Genetics"], "users"=>["Tobias Karlberg", "Susanne van den Berg", "Martin Hammarström", "Johanna Sagemark", "Ida Johansson", "Lovisa Holmberg-Schiavone", "Herwig Schüler"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006975.g003", "stats"=>{"downloads"=>11, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_paraplegin_ATPase_domain_structure_/549239", "title"=>"Overview of the paraplegin ATPase domain structure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-20 02:33:59"}

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  • {"unique-ip"=>"8", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
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  • {"unique-ip"=>"12", "full-text"=>"10", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
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  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
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  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"17", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"16", "full-text"=>"9", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
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  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
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  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
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  • {"unique-ip"=>"22", "full-text"=>"18", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"13", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
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  • {"unique-ip"=>"20", "full-text"=>"20", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"17", "full-text"=>"18", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"19", "full-text"=>"15", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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  • {"unique-ip"=>"22", "full-text"=>"16", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"16", "full-text"=>"13", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"13", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"12", "full-text"=>"13", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"15", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"22", "full-text"=>"20", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"14", "full-text"=>"8", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"20", "full-text"=>"16", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
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Relative Metric

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