X-Ray Structure Reveals a New Class and Provides Insight into Evolution of Alkaline Phosphatases
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{"title"=>"X-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases", "type"=>"journal", "authors"=>[{"first_name"=>"Subhash C.", "last_name"=>"Bihani", "scopus_author_id"=>"26027745200"}, {"first_name"=>"Amit", "last_name"=>"Das", "scopus_author_id"=>"55628533748"}, {"first_name"=>"Kayzad S.", "last_name"=>"Nilgiriwala", "scopus_author_id"=>"24765391000"}, {"first_name"=>"Vishal", "last_name"=>"Prashar", "scopus_author_id"=>"8599047100"}, {"first_name"=>"Michel", "last_name"=>"Pirocchi", "scopus_author_id"=>"6507735568"}, {"first_name"=>"Shree Kumar", "last_name"=>"Apte", "scopus_author_id"=>"7101907189"}, {"first_name"=>"Jean Luc", "last_name"=>"Ferrer", "scopus_author_id"=>"35473126500"}, {"first_name"=>"Madhusoodan V.", "last_name"=>"Hosur", "scopus_author_id"=>"56250008400"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21829507", "doi"=>"10.1371/journal.pone.0022767", "issn"=>"19326203", "scopus"=>"2-s2.0-79960871721", "pui"=>"362231727", "sgr"=>"79960871721"}, "id"=>"2d632ab3-de41-3fa6-987b-9e26230719fa", "abstract"=>"The alkaline phosphatase (AP) is a bi-metalloenzyme of potential applications in biotechnology and bioremediation, in which phosphate monoesters are nonspecifically hydrolysed under alkaline conditions to yield inorganic phosphate. The hydrolysis occurs through an enzyme intermediate in which the catalytic residue is phosphorylated. The reaction, which also requires a third metal ion, is proposed to proceed through a mechanism of in-line displacement involving a trigonal bipyramidal transition state. Stabilizing the transition state by bidentate hydrogen bonding has been suggested to be the reason for conservation of an arginine residue in the active site. We report here the first crystal structure of alkaline phosphatase purified from the bacterium Sphingomonas. sp. Strain BSAR-1 (SPAP). The crystal structure reveals many differences from other APs: 1) the catalytic residue is a threonine instead of serine, 2) there is no third metal ion binding pocket, and 3) the arginine residue forming bidentate hydrogen bonding is deleted in SPAP. A lysine and an aspargine residue, recruited together for the first time into the active site, bind the substrate phosphoryl group in a manner not observed before in any other AP. These and other structural features suggest that SPAP represents a new class of APs. Because of its direct contact with the substrate phosphoryl group, the lysine residue is proposed to play a significant role in catalysis. The structure is consistent with a mechanism of in-line displacement via a trigonal bipyramidal transition state. The structure provides important insights into evolutionary relationships between members of AP superfamily.", "link"=>"http://www.mendeley.com/research/xray-structure-reveals-new-class-provides-insight-evolution-alkaline-phosphatases", "reader_count"=>17, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>6, "Student > Ph. D. Student"=>2, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>6, "Student > Ph. D. Student"=>2, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"India"=>3}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/751753"], "description"=>"<p>Absolutely conserved residues are shown in red. Three interesting facts are highlighted by black arrows: 1) presence of Thr89 in place of catalytic serine, 2) presence of novel Arg173 and 3) deletion, in SPAP, of conserved arginine.</p>", "links"=>[], "tags"=>["alignment", "derived", "superposition", "alkaline"], "article_id"=>422114, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g008", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_alignment_derived_from_structural_superposition_of_alkaline_phosphatases_/422114", "title"=>"Sequence alignment derived from structural superposition of alkaline phosphatases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:18:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/751535"], "description"=>"<p>Note that Thr89 hydroxyl overlaps the ester oxygen in the phosphoenzyme complex.</p>", "links"=>[], "tags"=>["hydroxyl", "catalytic", "residues", "superposition", "phosphoenzyme", "intermediate"], "article_id"=>421891, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g006", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_orientation_of_hydroxyl_group_of_catalytic_residues_at_different_stages_structural_superposition_in_present_structure_magenta_phosphoenzyme_intermediate_green_and_product_complex_light_blue_/421891", "title"=>"Relative orientation of hydroxyl group of catalytic residues at different stages: structural superposition in present structure (magenta), phosphoenzyme intermediate (green) and product complex (light blue).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:17:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/752107"], "description"=>"<p>*The numbers between parentheses indicate the value in the outer resolution shell. R.m.s =  root mean square.</p>", "links"=>[], "tags"=>["chemistry", "biotechnology", "Evolutionary biology", "physics", "Biochemistry"], "article_id"=>422469, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.t002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Refinement_statistics_for_native_SPAP_/422469", "title"=>"Refinement statistics for native SPAP.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 16:20:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/751660"], "description"=>"<p>(A) amino acid substitutions that abolish Mg<sup>2+</sup> binding site in SPAP. (B) Comparision of interactions of Mg<sup>2+</sup> (ECAP) and Lys171 (SPAP) with substrate phosphate and active site aspartate.</p>", "links"=>[], "tags"=>["substitute", "superposition", "spap", "ecap"], "article_id"=>422023, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g007", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lys171_in_SPAP_a_substitute_for_third_metal_Superposition_of_SPAP_magenta_and_ECAP_cyan_/422023", "title"=>"Lys171 in SPAP, a substitute for third metal: Superposition of SPAP (magenta) and ECAP (cyan).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:18:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/751126"], "description"=>"<p>The oxygen atom (O3) from the substrate-phosphate is shown in red.</p>", "links"=>[], "tags"=>["co-ordination", "zinc", "ions", "residues", "substrate"], "article_id"=>421482, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g003", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Active_site_geometry_co_ordination_of_zinc_metal_ions_slate_to_protein_residues_magenta_and_to_the_substrate_in_the_active_site_/421482", "title"=>"Active site geometry: co-ordination of zinc metal ions (slate) to protein residues (magenta) and to the substrate in the active site.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:12:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/751279"], "description"=>"<p>Green contours are for the mFo – DFc map contoured at 3.0 σ level. Blue contrours are for the 2mFo – DFc map contoured at 0.8 σ level.</p>", "links"=>[], "tags"=>["electron", "r-o-po3", "monoester"], "article_id"=>421644, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g004", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Michaeli_s_complex_electron_density_for_the_R_O_PO3_monoester_substrate_/421644", "title"=>"Michaeli's complex: electron density for the R-O-PO3 monoester substrate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:16:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/752145"], "description"=>"<p>Metal coordination distances in SPAP and ECAP.</p>", "links"=>[], "tags"=>["coordination", "distances", "spap"], "article_id"=>422510, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.t003", "stats"=>{"downloads"=>5, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metal_coordination_distances_in_SPAP_and_ECAP_/422510", "title"=>"Metal coordination distances in SPAP and ECAP.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 16:20:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/751949"], "description"=>"<p>Distances are in Å unit.</p>", "links"=>[], "tags"=>["hydrogen", "bonding", "interactions", "involving", "his93", "asp300", "od1", "correlated", "differences", "spap", "ecap"], "article_id"=>422287, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g009", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Novel_hydrogen_bonding_interactions_in_SPAP_A_Hydrogen_bonding_network_involving_His93_B_Conservation_of_hydrogen_bond_from_Asp300_OD1_through_correlated_sequence_differences_in_SPAP_pink_and_ECAP_slate_/422287", "title"=>"Novel hydrogen bonding interactions in SPAP: (A) Hydrogen bonding network involving His93 (B) Conservation of hydrogen bond from Asp300 OD1 through correlated sequence differences in SPAP (pink) and ECAP (slate).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:19:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/752186"], "description"=>"<p>The numbers between parentheses indicate the value in the outer resolution shell.</p>", "links"=>[], "tags"=>["collections", "phasing"], "article_id"=>422547, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_collections_and_phasing_statistics_for_SM_SPAP_/422547", "title"=>"Data collections and phasing statistics for SM-SPAP.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 16:20:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/752220"], "description"=>"<p>Number of SS elements aligned  =  12.</p><p>Maximum number of residues aligned  =  233.</p>", "links"=>[], "tags"=>["spap"], "article_id"=>422595, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.t004", "stats"=>{"downloads"=>10, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_comparison_of_SPAP_with_other_APs_only_C_945_s_are_used_to_superpose_/422595", "title"=>"Structural comparison of SPAP with other APs; only C<sub>α</sub>'s are used to superpose.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 16:21:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/750964"], "description"=>"<p>Standards used are shown in red along with their molecular weights. SPAP, shown in blue, elutes as a monomer of molecular weight 58 kD.</p>", "links"=>[], "tags"=>["exclusion", "chromatography", "elution"], "article_id"=>421331, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Size_Exclusion_Chromatography_Elution_profile_of_SPAP_/421331", "title"=>"Size Exclusion Chromatography Elution profile of SPAP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:11:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/752039"], "description"=>"<p>Note that SPAP and ECAP-like AP's are on different branches of evolution tree. Also SPAP and NPP are predicted to have a common ancestor.</p>", "links"=>[], "tags"=>["superposition", "ccladogram", "evolutionary", "ap", "superfamily", "spap"], "article_id"=>422397, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g010", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_superposition_based_cCladogram_showing_evolutionary_relationship_within_AP_superfamily_ECAP_like_APs_SPAP_and_NPP_/422397", "title"=>"Structural superposition based cCladogram showing evolutionary relationship within AP superfamily (ECAP like APs, SPAP and NPP).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:20:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/750869"], "description"=>"<p>Unique disulfide bond near the active site: unique disulfide bond Cys90 – Cys126 next to the catalytic residue Thr89 may be crucial for the integrity of active site geometry.</p>", "links"=>[], "tags"=>["disulfide", "cys90", "cys126", "catalytic", "residue", "thr89"], "article_id"=>421214, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unique_disulfide_bond_near_the_active_site_unique_disulfide_bond_Cys90_8211_Cys126_next_to_the_catalytic_residue_Thr89_may_be_crucial_for_the_integrity_of_active_site_geometry_/421214", "title"=>"Unique disulfide bond near the active site: unique disulfide bond Cys90 – Cys126 next to the catalytic residue Thr89 may be crucial for the integrity of active site geometry.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:10:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/751418"], "description"=>"<p>Only SPAP has residues covering other members of the superfamily. (B) Phosphate interactions in the active site of SPAP. The distances given are in Å unit.</p>", "links"=>[], "tags"=>["phosphate", "moiety", "superposition", "residues", "binding", "substrate", "ap", "spap", "ecap", "npp", "ipgm"], "article_id"=>421765, "categories"=>["Physics", "Biotechnology", "Biochemistry", "Chemistry", "Evolutionary Biology"], "users"=>["Subhash C. Bihani", "Amit Das", "Kayzad S. Nilgiriwala", "Vishal Prashar", "Michel Pirocchi", "Shree Kumar Apte", "Jean-Luc Ferrer", "Madhusoodan V. Hosur"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022767.g005", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interactions_to_the_Phosphate_moiety_in_the_active_site_A_Structural_superposition_of_residues_binding_the_substrate_in_the_AP_superfamily_SPAP_Magenta_ECAP_slate_NPP_yellow_iPGM_green_/421765", "title"=>"Interactions to the Phosphate moiety in the active site: (A) Structural superposition of residues binding the substrate in the AP superfamily: SPAP (Magenta), ECAP (slate), NPP (yellow), iPGM (green).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:16:46"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"0", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"1"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"2"}
  • {"unique-ip"=>"5", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"3"}
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  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"4"}
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Relative Metric

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