Structural Evolution of the Protein Kinase–Like Superfamily
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{"title"=>"Structural Evolution of the Protein Kinase–Like Superfamily", "type"=>"journal", "authors"=>[{"first_name"=>"Eric D.", "last_name"=>"Scheeff"}, {"first_name"=>"Philip E.", "last_name"=>"Bourne"}], "year"=>2005, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"1553-734X", "scopus"=>"2-s2.0-41849110846", "pui"=>"135774937", "doi"=>"10.1371/journal.pcbi.0010049", "isbn"=>"1553-734X\\n1553-7358", "sgr"=>"41849110846", "pmid"=>"16244704"}, "id"=>"e94372a6-19c8-35ad-90d0-5231ea5571c9", "abstract"=>"The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase-like superfamily. The comparison of structures revealed a \"universal core\" domain consisting only of regions required for ATP binding and the phosphotransfer reaction. Remarkably, even within the universal core some kinase structures display notable changes, while still retaining essential activity. Hence, the protein kinase-like superfamily has undergone substantial structural and sequence revision over long evolutionary timescales. We constructed a phylogenetic tree for the superfamily using a novel approach that allowed for the combination of sequence and structure information into a unified quantitative analysis. When considered against the backdrop of species distribution and other metrics, our tree provides a compelling scenario for the development of the various kinase families from a shared common ancestor. We propose that most of the so-called \"atypical kinases\" are not intermittently derived from protein kinases, but rather diverged early in evolution to form a distinct phyletic group. Within the atypical kinases, the aminoglycoside and choline kinase families appear to share the closest relationship. These two families in turn appear to be the most closely related to the protein kinase family. In addition, our analysis suggests that the actin-fragmin kinase, an atypical protein kinase, is more closely related to the phosphoinositide-3 kinase family than to the protein kinase family. The two most divergent families, alpha-kinases and phosphatidylinositol phosphate kinases (PIPKs), appear to have distinct evolutionary histories. While the PIPKs probably have an evolutionary relationship with the rest of the kinase superfamily, the relationship appears to be very distant (and perhaps indirect). Conversely, the alpha-kinases appear to be an exception to the scenario of early divergence for the atypical kinases: they apparently arose relatively recently in eukaryotes. We present possible scenarios for the derivation of the alpha-kinases from an extant kinase fold.", "link"=>"http://www.mendeley.com/research/structural-evolution-protein-kinaselike-superfamily", "reader_count"=>234, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>12, "Researcher"=>78, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>59, "Student > Postgraduate"=>10, "Student > Master"=>25, "Other"=>4, "Student > Bachelor"=>24, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>12, "Researcher"=>78, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>59, "Student > Postgraduate"=>10, "Student > Master"=>25, "Other"=>4, "Student > Bachelor"=>24, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Agricultural and Biological Sciences"=>138, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>21, "Computer Science"=>10, "Earth and Planetary Sciences"=>1, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>38, "Medicine and Dentistry"=>5, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>3, "Social Sciences"=>1, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>21}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>138}, "Computer Science"=>{"Computer Science"=>10}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>38}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Romania"=>1, "United States"=>17, "United Kingdom"=>6, "Thailand"=>1, "Spain"=>1, "India"=>1, "Czech Republic"=>1, "Belgium"=>1, "Norway"=>1, "China"=>1, "Brazil"=>1, "Mexico"=>2, "Israel"=>1, "France"=>2, "Germany"=>3}, "group_count"=>7}

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  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"67"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"22", "xml_views"=>"1", "html_views"=>"96"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"21", "xml_views"=>"1", "html_views"=>"81"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"69"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"18", "xml_views"=>"0", "html_views"=>"35"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"43"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"25", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"34"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"19", "xml_views"=>"2", "html_views"=>"44"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"15"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"4", "html_views"=>"30"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"18", "xml_views"=>"2", "html_views"=>"34"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"20", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"1", "html_views"=>"42"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"15", "xml_views"=>"1", "html_views"=>"26"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"27", "xml_views"=>"0", "html_views"=>"37"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"52"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"14", "xml_views"=>"3", "html_views"=>"36"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"29", "xml_views"=>"1", "html_views"=>"40"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"25", "xml_views"=>"1", "html_views"=>"39"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"20", "xml_views"=>"1", "html_views"=>"47"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"22"}
  • {"month"=>"10", "year"=>"2019", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"36"}
  • {"month"=>"11", "year"=>"2019", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"26"}
  • {"month"=>"12", "year"=>"2019", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"1", "year"=>"2020", "pdf_views"=>"20", "xml_views"=>"0", "html_views"=>"24"}
  • {"month"=>"2", "year"=>"2020", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"3", "year"=>"2020", "pdf_views"=>"23", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"4", "year"=>"2020", "pdf_views"=>"56", "xml_views"=>"2", "html_views"=>"54"}
  • {"month"=>"5", "year"=>"2020", "pdf_views"=>"42", "xml_views"=>"0", "html_views"=>"25"}
  • {"month"=>"6", "year"=>"2020", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"7", "year"=>"2020", "pdf_views"=>"18", "xml_views"=>"1", "html_views"=>"13"}
  • {"month"=>"8", "year"=>"2020", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"8"}
  • {"month"=>"9", "year"=>"2020", "pdf_views"=>"8", "xml_views"=>"1", "html_views"=>"15"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/961432"], "description"=>"<p>Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives</p>", "links"=>[], "tags"=>["alignment", "derived"], "article_id"=>631424, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g303", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enhanced_Sequence_Alignment_Derived_from_the_Structural_Alignment_of_Kinase_Representatives_/631424", "title"=>"Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:57:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/961853"], "description"=>"<p>This tree did not explicitly incorporate structural information, and is\n\t\t\t\t\t\t\tprovided for purposes of comparison with the Bayesian tree presented in\n\t\t\t\t\t\t\t\t<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g004\" target=\"_blank\">Figure 4</a>.\n\t\t\t\t\t\t\tStructures are labeled by their PDB IDs, followed by the abbreviated\n\t\t\t\t\t\t\tname of the structure. The AKs are highlighted by orange ovals.\n\t\t\t\t\t\t\tBootstrap values are provided for major branches. Some branches are too\n\t\t\t\t\t\t\tshort for values to fit; these are marked with red letters that\n\t\t\t\t\t\t\tcorrespond to the following values: a, 199; b, 170; c, 101; d, 141.\n\t\t\t\t\t\t\tBranches highlighted in gray were not supported by bootstrap values\n\t\t\t\t\t\t\tabove 500, and should be considered speculative (if based only on this\n\t\t\t\t\t\t\ttree data) [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b57\" target=\"_blank\">57</a>,<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b58\" target=\"_blank\">58</a>]. Many of the core relationships within the\n\t\t\t\t\t\t\tsuperfamily cannot be resolved with confidence using the conventional\n\t\t\t\t\t\t\tsequence-based approach.</p>", "links"=>[], "tags"=>["distance-based", "phylogenetic", "alignment"], "article_id"=>631841, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conventional_Distance_Based_Phylogenetic_Tree_of_the_Kinase_Like_Superfamily_Based_Only_on_the_Sequence_Alignment_from_Figure_3_/631841", "title"=>"Conventional Distance-Based Phylogenetic Tree of the Kinase-Like\n\t\t\t\t\t\t\tSuperfamily, Based Only on the Sequence Alignment from Figure 3", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:00:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/961307"], "description"=>"<p>Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives</p>", "links"=>[], "tags"=>["alignment", "derived"], "article_id"=>631299, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g302", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enhanced_Sequence_Alignment_Derived_from_the_Structural_Alignment_of_Kinase_Representatives_/631299", "title"=>"Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:56:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/961175"], "description"=>"<p>Abbreviated names of kinase representatives are provided with the gray box at\n\t\t\t\t\t\tthe left-hand side of the figure (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-t001\" target=\"_blank\">Table 1</a> for more information on\n\t\t\t\t\t\tstructures). The name is followed by the PDB ID [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b18\" target=\"_blank\">18</a>] for the\n\t\t\t\t\t\tstructure used in the alignment. The number in parenthesis following the PDB\n\t\t\t\t\t\tID is the residue number of the first residue shown in the alignment. The\n\t\t\t\t\t\tsequences of the six AKs are clustered at the top of the alignment, followed\n\t\t\t\t\t\tby the sequence of PKA, which is highlighted. The alignment is annotated for\n\t\t\t\t\t\tkey structural features using the JOY software [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b78\" target=\"_blank\">78</a>]. Secondary\n\t\t\t\t\t\tstructure is represented using the following conventions: light-gray box,\n\t\t\t\t\t\tβ-strand; medium-gray box, 3–10 helix; dark-gray box,\n\t\t\t\t\t\tα-helix. Residue characteristics are represented using the\n\t\t\t\t\t\tfollowing conventions: uppercase, solvent inaccessible; lowercase, solvent\n\t\t\t\t\t\taccessible; bold, hydrogen bond to main chain amide; underline, hydrogen\n\t\t\t\t\t\tbond to main chain carbonyl; tilde, hydrogen bond to other side-chain;\n\t\t\t\t\t\titalic, positive Φ; breve, <i>cis</i>-peptide. Residues\n\t\t\t\t\t\tthat are highly conserved within the TPK family and some AKs are highlighted\n\t\t\t\t\t\tin boxes for the sequences where the conservation applies. The residue(s)\n\t\t\t\t\t\tseen at these positions are shown in uppercase above the boxes. The letter O\n\t\t\t\t\t\tstands for general hydrophobicity, but not a specific residue type. Residues\n\t\t\t\t\t\tthat are more weakly conserved in the TPKs but are also conserved in many\n\t\t\t\t\t\tother AK families are noted with a lowercase letter above the appropriate\n\t\t\t\t\t\talignment columns. Selected residues of interest that are conserved only\n\t\t\t\t\t\twithin the TPKs are depicted using the same conventions above, but with gray\n\t\t\t\t\t\tlettering (depiction of residues conserved only in the TPKs is not\n\t\t\t\t\t\texhaustive, i.e., only residues discussed in the text are highlighted above\n\t\t\t\t\t\tthe alignment. Generally, this is done in structural regions unique to the\n\t\t\t\t\t\tTPKs). Secondary structures are labeled with the nomenclature used for PKA\n\t\t\t\t\t\t\t[<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b12\" target=\"_blank\">12</a>]. Sequence representing unresolved portions of the\n\t\t\t\t\t\tstructure is not shown by JOY. In key portions of the alignment, this\n\t\t\t\t\t\tsequence is added back in and shown in light gray.</p>", "links"=>[], "tags"=>["alignment", "derived"], "article_id"=>631172, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g301", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enhanced_Sequence_Alignment_Derived_from_the_Structural_Alignment_of_Kinase_Representatives_/631172", "title"=>"Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/961602"], "description"=>"<p>Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives</p>", "links"=>[], "tags"=>["alignment", "derived"], "article_id"=>631593, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g304", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enhanced_Sequence_Alignment_Derived_from_the_Structural_Alignment_of_Kinase_Representatives_/631593", "title"=>"Enhanced Sequence Alignment Derived from the Structural Alignment of\n\t\t\t\t\t\tKinase Representatives", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:58:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/961770"], "description"=>"<p>Colors and nomenclature for secondary structural elements are\n\t\t\t\t\t\t\t\tidentical to those provided in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g002\" target=\"_blank\">Figure 2</a>. Structures shown are\n\t\t\t\t\t\t\t\tthe C-terminal subdomains of four structures: (A) PKA\n\t\t\t\t\t\t\t\t\t[<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b70\" target=\"_blank\">70</a>]; (B) CKA-2 [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b23\" target=\"_blank\">23</a>]; (C) PI3K\n\t\t\t\t\t\t\t\t\t[<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b21\" target=\"_blank\">21</a>]; and (D) AFK [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b22\" target=\"_blank\">22</a>]. For clarity, some\n\t\t\t\t\t\t\t\tportions of structures are omitted. Residues involved in the shared\n\t\t\t\t\t\t\t\thydrogen-bond networks are shown in a ball-and-stick rendering. For\n\t\t\t\t\t\t\t\tclarity, side-chains are omitted for residues that only participate\n\t\t\t\t\t\t\t\tin the network via backbone interactions. Residues involved directly\n\t\t\t\t\t\t\t\tin catalysis or metal binding are shown with light-green stick\n\t\t\t\t\t\t\t\tregions in the ball-and-stick rendering. Metal atoms, when present,\n\t\t\t\t\t\t\t\tare shown as gray spheres. ATP (or ATP analog), when present, is\n\t\t\t\t\t\t\t\tshown in a line rendering. Hydrogen bonds are shown in cyan. The\n\t\t\t\t\t\t\t\torientation of the structures is similar but not identical\n\t\t\t\t\t\t\t\t(structures were rotated somewhat to make H-bond contacts more\n\t\t\t\t\t\t\t\tvisible). Molecular renderings in this figure were created with\n\t\t\t\t\t\t\t\tMOLSCRIPT [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b90\" target=\"_blank\">90</a>].</p>", "links"=>[], "tags"=>["hydrogen-bonding", "networks", "distantly", "kinase-like"], "article_id"=>631758, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g005", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Shared_Hydrogen_Bonding_Networks_between_Distantly_Related__Structures_in_the_Kinase_Like_Superfamily_/631758", "title"=>"Shared Hydrogen-Bonding Networks between Distantly Related\n\t\t\t\t\t\t\t\tStructures in the Kinase-Like Superfamily", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:59:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/961020"], "description"=>"<p>Structures are shown in an open-face view, and using the same conventions as\n\t\t\t\t\t\tused for PKA in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001\" target=\"_blank\">Figure\n\t\t\t\t\t\t1</a>. ATP and metal ions are shown in mirror image where available in\n\t\t\t\t\t\tthe structure. Similar to <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001\" target=\"_blank\">Figure 1</a>, secondary structural elements are colored according to\n\t\t\t\t\t\ttheir conservation status in the overall superfamily as follows: yellow,\n\t\t\t\t\t\telements are part of the “universal core” seen in all\n\t\t\t\t\t\tkinases in the superfamily; orange, elements are present in more than two,\n\t\t\t\t\t\tbut not all, of the kinases in the superfamily; red, elements shared between\n\t\t\t\t\t\tonly two families; purple, elements seen only in this family, but inserted\n\t\t\t\t\t\twithin in the portion of the chain forming the universal core; blue,\n\t\t\t\t\t\telements seen only in this family, and connected to the N- or C-terminal\n\t\t\t\t\t\tends of the universal core. Secondary structural elements are labeled\n\t\t\t\t\t\taccording to the standard conventions for the individual structure. As in\n\t\t\t\t\t\t\t<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001\" target=\"_blank\">Figure 1</a>, the\n\t\t\t\t\t\tglycine-rich loop is rendered in green and the loop forming the linker\n\t\t\t\t\t\tregion is rendered in red. For clarity, the conserved residues shown in\n\t\t\t\t\t\t\t<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001\" target=\"_blank\">Figure 1</a> are not\n\t\t\t\t\t\trendered in these structures, though in most cases they are similar.\n\t\t\t\t\t\tStructures shown are as follows: (A) aminoglycoside phosphotransferase\n\t\t\t\t\t\t(APH(3′)-IIIa [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b24\" target=\"_blank\">24</a>]); (B) CK (CKA-2\n\t\t\t\t\t\t\t[<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b23\" target=\"_blank\">23</a>]); (C) ChaK [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b20\" target=\"_blank\">20</a>]; (D) PI3K [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b21\" target=\"_blank\">21</a>]; (E) AFK\n\t\t\t\t\t\t\t[<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b22\" target=\"_blank\">22</a>]; and (F) PIPKIIβ [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b19\" target=\"_blank\">19</a>]. Molecular\n\t\t\t\t\t\trenderings in this figure were created with MOLSCRIPT [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b90\" target=\"_blank\">90</a>].</p>", "links"=>[], "tags"=>["representatives"], "article_id"=>631023, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Views_of_Structural_Representatives_from_Six_Families_in_the_Kinase_Like_Superfamily_Other_Than_the_TPKs_/631023", "title"=>"Views of Structural Representatives from Six Families in the Kinase-Like\n\t\t\t\t\t\tSuperfamily Other Than the TPKs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:54:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/472215", "https://ndownloader.figshare.com/files/472273"], "description"=>"<div><p>The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase–like superfamily. The comparison of structures revealed a “universal core” domain consisting only of regions required for ATP binding and the phosphotransfer reaction. Remarkably, even within the universal core some kinase structures display notable changes, while still retaining essential activity. Hence, the protein kinase–like superfamily has undergone substantial structural and sequence revision over long evolutionary timescales. We constructed a phylogenetic tree for the superfamily using a novel approach that allowed for the combination of sequence and structure information into a unified quantitative analysis. When considered against the backdrop of species distribution and other metrics, our tree provides a compelling scenario for the development of the various kinase families from a shared common ancestor. We propose that most of the so-called “atypical kinases” are not intermittently derived from protein kinases, but rather diverged early in evolution to form a distinct phyletic group. Within the atypical kinases, the aminoglycoside and choline kinase families appear to share the closest relationship. These two families in turn appear to be the most closely related to the protein kinase family. In addition, our analysis suggests that the actin-fragmin kinase, an atypical protein kinase, is more closely related to the phosphoinositide-3 kinase family than to the protein kinase family. The two most divergent families, α-kinases and phosphatidylinositol phosphate kinases (PIPKs), appear to have distinct evolutionary histories. While the PIPKs probably have an evolutionary relationship with the rest of the kinase superfamily, the relationship appears to be very distant (and perhaps indirect). Conversely, the α-kinases appear to be an exception to the scenario of early divergence for the atypical kinases: they apparently arose relatively recently in eukaryotes. We present possible scenarios for the derivation of the α-kinases from an extant kinase fold.</p></div>", "links"=>[], "tags"=>["superfamily"], "article_id"=>153112, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.0010049.sg001", "https://dx.doi.org/10.1371/journal.pcbi.0010049.sg002"], "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Structural_Evolution_of_the_Protein_Kinase_Like_Superfamily/153112", "title"=>"Structural Evolution of the Protein Kinase–Like Superfamily", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-20 10:52:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/961688"], "description"=>"<p>Structures are labeled by their PDB IDs, followed by the abbreviated name\n\t\t\t\t\t\t\tof the structure. TPKs are to the left of the figure, and are labeled\n\t\t\t\t\t\t\twith their group membership. TPKs labeled with a black asterisk are\n\t\t\t\t\t\t\tclassified differently in our tree compared with the classification\n\t\t\t\t\t\t\tproduced by Manning et al<i>.</i> [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b07\" target=\"_blank\">7</a>]. The AKs\n\t\t\t\t\t\t\tare highlighted with an orange oval. Major branches are labeled with\n\t\t\t\t\t\t\ttheir posterior probabilities. Gray ovals represent areas of doubt in\n\t\t\t\t\t\t\tthe tree, based on the tree itself and other aspects of our analysis\n\t\t\t\t\t\t\t(see text). The left-hand oval represents uncertainty as to the closest\n\t\t\t\t\t\t\tTPK relative to the AKs; it is unclear where precisely the AKs should\n\t\t\t\t\t\t\tlink to the TPKs (note that this uncertainty does not include the\n\t\t\t\t\t\t\tbranching of most of the TPK groups in this region, as these are\n\t\t\t\t\t\t\tgenerally well supported). The right-hand oval represents uncertainty as\n\t\t\t\t\t\t\tto the proper placement of ChaK and PIPKIIβ. These kinases are\n\t\t\t\t\t\t\tdifficult to place with high confidence because of their extreme\n\t\t\t\t\t\t\tdivergence. They are labeled with red asterisks to denote the\n\t\t\t\t\t\t\tspeculative nature of the current placement (see text).</p>", "links"=>[], "tags"=>["phylogeny", "kinase-like", "bayesian", "alignment", "matrix"], "article_id"=>631673, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proposed_Phylogeny_for_the_Kinase_Like_Superfamily_Based_on_a_Unified_Bayesian_Analysis_of_Both_the_Sequence_Alignment_in_Figure_3_and_the_Structural_Character_Matrix_in_Table_2_/631673", "title"=>"Proposed Phylogeny for the Kinase-Like Superfamily, Based on a\n\t\t\t\t\t\t\tUnified Bayesian Analysis of Both the Sequence Alignment in Figure 3 and the\n\t\t\t\t\t\t\tStructural Character Matrix in Table 2", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:59:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/960900"], "description"=>"<p>The structure consists of two subdomains: a small, primarily β-sheet\n\t\t\t\t\t\tN-terminal subdomain, and a larger, primarily helical C-terminal subdomain.\n\t\t\t\t\t\tATP and metal ions are bound in the cleft between the two subdomains. The\n\t\t\t\t\t\tsmall left-side view depicts PKA in the “standard”\n\t\t\t\t\t\torientation used by the authors when the structure was initially solved\n\t\t\t\t\t\t\t[<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b12\" target=\"_blank\">12</a>], and in many subsequent publications. The larger view\n\t\t\t\t\t\ton the right side depicts PKA in an “open-book” format\n\t\t\t\t\t\tthat makes structural features in the two subdomains easier to compare\n\t\t\t\t\t\tbetween families. The open-book view is achieved by rotating the standard\n\t\t\t\t\t\tview 90° about the vertical axis, then splitting the two subdomains\n\t\t\t\t\t\tat the linker region and rotating each 90° in opposite directions\n\t\t\t\t\t\tabout the horizontal axis. Helical secondary structures (both\n\t\t\t\t\t\tα-helices and 3–10 helices) are depicted as cylinders,\n\t\t\t\t\t\tand β-strands are depicted as arrows. Elements are labeled\n\t\t\t\t\t\taccording to the standard conventions for PKA. Some secondary structure\n\t\t\t\t\t\t(particularly 3–10 helices) is not labeled in the standard PKA\n\t\t\t\t\t\tconvention, and so is unlabeled here. One structure (Helix 1) was named by\n\t\t\t\t\t\tus (see text). Underlined labels belong to helical structures;\n\t\t\t\t\t\tnon-underlined labels belong to β-strands. Secondary structure\n\t\t\t\t\t\telements are colored according to their conservation status in the overall\n\t\t\t\t\t\tsuperfamily as follows: yellow, elements are part of the\n\t\t\t\t\t\t“universal core” seen in all kinases in the superfamily;\n\t\t\t\t\t\torange, elements are present in more than two, but not all, of the kinases\n\t\t\t\t\t\tin the superfamily; purple, elements seen only in this family, but inserted\n\t\t\t\t\t\twithin in the portion of the chain forming the universal core; blue,\n\t\t\t\t\t\telements seen only in this family, and connected to the N- or C-terminal\n\t\t\t\t\t\tends of the universal core. A bound pseudosubstrate inhibitor (PKI) is\n\t\t\t\t\t\tpresent in the structure [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b12\" target=\"_blank\">12</a>], and depicted in gray. This\n\t\t\t\t\t\tinhibitor likely describes the binding location of actual substrates of PKA.\n\t\t\t\t\t\tThe bound ATP molecule is rendered as a ball-and-stick model, while the\n\t\t\t\t\t\tbound Mg ions are rendered as gray spheres. The ATP and Mg ions are\n\t\t\t\t\t\tduplicated in mirror image and shown interacting with both the N- and C-\n\t\t\t\t\t\tterminal subdomains in the open-book rendering. The most critical and highly\n\t\t\t\t\t\tconserved residues in PKA (and the broader superfamily) are shown as\n\t\t\t\t\t\tball-and-stick models in green, and labeled according to the standard PKA\n\t\t\t\t\t\tnumbering scheme. In addition, the glycine-rich loop is also depicted in\n\t\t\t\t\t\tgreen, though individual glycine residues are not shown. The loop that forms\n\t\t\t\t\t\tthe linker region between the subdomains is depicted in red. Other loops\n\t\t\t\t\t\twithin the universal core are shown in white, except for loops linking\n\t\t\t\t\t\tpurple regions (which are shown in purple), and loops outside of the\n\t\t\t\t\t\tuniversal core (shown in blue). Key loops described extensively in the text\n\t\t\t\t\t\tare labeled. For increased clarity, residues 300–350 have been\n\t\t\t\t\t\tremoved from the C-terminus of PKA. This loop region is unique to PKA, and\n\t\t\t\t\t\twould have been colored blue if present in the figure. Molecular renderings\n\t\t\t\t\t\tin this figure were created with MOLSCRIPT [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b90\" target=\"_blank\">90</a>].</p>", "links"=>[], "tags"=>["views", "pka"], "article_id"=>630906, "categories"=>["Molecular Biology", "Biological Sciences", "Evolutionary Biology"], "users"=>["Eric D Scheeff", "Philip E Bourne"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0010049.g001", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_Views_of_the_Structure_of_PKA_70_/630906", "title"=>"Two Views of the Structure of PKA [70]", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:53:31"}

PMC Usage Stats | Further Information

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Relative Metric

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