Crystal Structure of an (R)-Selective ω-Transaminase from Aspergillus terreus
Publication Date
January 30, 2014
Journal
PLOS ONE
Authors
Andrzej Łyskowski, Christian Gruber, Georg Steinkellner, Martin Schürmann, et al
Volume
9
Issue
1
Pages
e87350
DOI
https://dx.plos.org/10.1371/journal.pone.0087350
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0087350
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24498081
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907554
Europe PMC
http://europepmc.org/abstract/MED/24498081
Web of Science
000330617100077
Mendeley
http://www.mendeley.com/research/crystal-structure-rselective-%CF%89transaminase-aspergillus-terreus
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Mendeley | Further Information

{"title"=>"Crystal Structure of an (R)-Selective ω-Transaminase from Aspergillus terreus", "type"=>"journal", "authors"=>[{"first_name"=>"Andrzej", "last_name"=>"Łyskowski"}, {"first_name"=>"Christian", "last_name"=>"Gruber"}, {"first_name"=>"Georg", "last_name"=>"Steinkellner"}, {"first_name"=>"Martin", "last_name"=>"Schürmann"}, {"first_name"=>"Helmut", "last_name"=>"Schwab"}, {"first_name"=>"Karl", "last_name"=>"Gruber"}, {"first_name"=>"Kerstin", "last_name"=>"Steiner"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"1932-6203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24498081", "doi"=>"10.1371/journal.pone.0087350"}, "id"=>"cda0a7ee-20bb-38b9-be38-10f984d99010", "abstract"=>"Chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (PLP) as cofactor. In nature, (S)-selective amine transaminases are more abundant than the (R)-selective enzymes, and therefore more information concerning their structures is available. Here, we present the crystal structure of an (R)-ω-transaminase from Aspergillus terreus determined by X-ray crystallography at a resolution of 1.6 Å. The structure of the protein is a homodimer that displays the typical class IV fold of PLP-dependent aminotransferases. The PLP-cofactor observed in the structure is present in two states (i) covalently bound to the active site lysine (the internal aldimine form) and (ii) as substrate/product adduct (the external aldimine form) and free lysine. Docking studies revealed that (R)-transaminases follow a dual binding mode, in which the large binding pocket can harbour the bulky substituent of the amine or ketone substrate and the α-carboxylate of pyruvate or amino acids, and the small binding pocket accommodates the smaller substituent.", "link"=>"http://www.mendeley.com/research/crystal-structure-rselective-%CF%89transaminase-aspergillus-terreus", "reader_count"=>62, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>28, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>28, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>30, "Chemical Engineering"=>3, "Chemistry"=>15}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>15}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>5}, "Chemical Engineering"=>{"Chemical Engineering"=>3}}, "reader_count_by_country"=>{"Netherlands"=>1, "United Kingdom"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1368348"], "description"=>"<p>The relative activities are referred to either the wild-type activity with pyruvate (0.8 U/mg lysate, dark grey bars) or butanal (0.1 U/mg lysate, light grey bars).</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "activities", "calculated", "acetophenone", "mutants", "thereof", "mm", "pyruvate", "50", "ph", "lysate"], "article_id"=>919552, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g007", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_activities_calculated_from_the_increase_of_acetophenone_at_300_TA_and_mutants_thereof_0_1_mM_PLP_5_mM_R_methylbenzylamine_5_mM_pyruvate_or_5_mM_butanal_in_50_mM_KPi_pH_7_5_0_25_mg_mL_of_total_lysate_protein_at_25_C_/919552", "title"=>"Relative activities calculated from the increase of acetophenone at 300-ωTA and mutants thereof (0.1 mM PLP, 5 mM <i>(R)-</i>α-methylbenzylamine, 5 mM pyruvate or 5 mM butanal, in 50 mM KPi, pH 7.5, 0.25 mg/mL of total lysate protein) at 25°C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368349"], "description"=>"a<p>defined by the substrate size, in some structures the actual difference in the size of the pockets is very subtle.</p>b<p>proposed binding as seen in the scheme in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087350#pone-0087350-g006\" target=\"_blank\">Figure 6</a>.</p>c<p>as observed in the solved structure of AT-ωTA.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "binding", "plp", "substituents", "amino", "amine", "transaminases", "iv"], "article_id"=>919553, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.t002", "stats"=>{"downloads"=>7, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localisation_of_the_large_and_small_binding_pocket_relative_to_PO_4_and_O3_8217_of_PLP_and_binding_of_the_substrates_8217_substituents_in_different_amino_acid_and_amine_transaminases_upper_part_fold_I_aminotransferases_lower_part_fold_IV_aminotransferase/919553", "title"=>"Localisation of the large and small binding pocket relative to PO<sub>4</sub> and O3’ of PLP and binding of the substrates’ substituents in different amino acid and amine transaminases (upper part: fold I aminotransferases, lower part: fold IV aminotransferases).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368350"], "description"=>"<p>Values in parentheses are for the highest resolution shell.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "refinement"], "article_id"=>919554, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_collection_and_refinement_statistics_/919554", "title"=>"Data collection and refinement statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368351"], "description"=>"<div><p>Chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5′-phosphate (PLP) as cofactor. In nature, (<i>S</i>)-selective amine transaminases are more abundant than the (<i>R</i>)-selective enzymes, and therefore more information concerning their structures is available. Here, we present the crystal structure of an (<i>R</i>)-ω-transaminase from <i>Aspergillus terreus</i> determined by X-ray crystallography at a resolution of 1.6 Å. The structure of the protein is a homodimer that displays the typical class IV fold of PLP-dependent aminotransferases. The PLP-cofactor observed in the structure is present in two states (i) covalently bound to the active site lysine (the internal aldimine form) and (ii) as substrate/product adduct (the external aldimine form) and free lysine. Docking studies revealed that (<i>R</i>)-transaminases follow a dual binding mode, in which the large binding pocket can harbour the bulky substituent of the amine or ketone substrate and the α-carboxylate of pyruvate or amino acids, and the small binding pocket accommodates the smaller substituent.</p></div>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography"], "article_id"=>919555, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350", "stats"=>{"downloads"=>16, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Crystal_Structure_of_an_R_Selective_Transaminase_from_Aspergillus_terreus_/919555", "title"=>"Crystal Structure of an (<i>R</i>)-Selective ω-Transaminase from <i>Aspergillus terreus</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368341"], "description"=>"<p>Detailed reaction mechanism of transaminases.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography"], "article_id"=>919545, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g001", "stats"=>{"downloads"=>5, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_reaction_mechanism_of_transaminases_/919545", "title"=>"Detailed reaction mechanism of transaminases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368342"], "description"=>"<p>A: Overview of the AT-ωTA dimer (chain A in green, chain B in grey), conserved regions are indicated in yellow, B: overview of the AT-ωTA dimer with the binding pockets indicated as orange spheres, C: small binding pocket amino acids (blue), D: large binding pocket amino acids (orange), E: PLP binding amino acids (green). The figures were prepared using the program PyMOL.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography"], "article_id"=>919546, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystal_structure_of_AT_969_TA_/919546", "title"=>"Crystal structure of AT-ωTA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368344"], "description"=>"<p>For PDB-IDs see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087350#pone.0087350.s001\" target=\"_blank\">Figure S2 in File S1</a>. The figure was prepared using the program PyMOL.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "thr121-val136", "alignment", "iv", "transaminase", "structures"], "article_id"=>919548, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Zoom_into_the_loop_Thr121_Val136_region_of_chain_B_in_the_structural_alignment_of_the_AT_969_TA_structure_magenta_with_other_fold_class_IV_transaminase_structures_dark_grey_/919548", "title"=>"Zoom into the loop Thr121-Val136 region of chain B in the structural alignment of the AT-ωTA structure (magenta) with other fold class IV transaminase structures (dark grey).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368345"], "description"=>"<p>A: Pro-(<i>R</i>)- and (<i>S</i>)-acetophenone pyridoxal phosphate intermediates docked into the active site of AT-ωTA. Green: amino acids of the active site (chain A) and PLP bound to K180, blue: amino acids of the active site (chain B), purple: pro-(<i>R</i>)-acetophenone pyridoxal phosphate intermediate, turquoise: pro-(<i>S</i>)-acetophenone pyridoxal phosphate intermediate. B: Acetophenone pyridoxal phosphate intermediate (purple), propiophenone pyridoxal phosphate intermediate (blue), butyrophenone pyridoxal phosphate intermediate (turquoise) docked into the active site of AT-ωTA compared to PLP bound to K180 in the structure of AT-ωTA (green). Green: amino acids of the active site (chain A), blue: amino acids of the active site (chain B). The figures were prepared using the program PyMOL.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "substrate", "intermediates"], "article_id"=>919549, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Docking_of_various_substrate_intermediates_into_AT_969_TA_/919549", "title"=>"Docking of various substrate intermediates into AT-ωTA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368346"], "description"=>"<p>A: Position of lysine relative to PLP in fold IV transaminases: in AT-ωTA (green), BCAT from human (1KT8, blue) or <i>E. coli</i> (1IYE, turquoise) and D-ATA from <i>Bacillus</i> sp. YM-1 (3DAA, brown). Ligands: blue: L-Ile-aldimine bound in human BCAT, turquoise: L-Glu-aldimine bound in BCAT from <i>E. coli</i>, brown: D-Ala-aldimine bound in D-ATA, green: L-Glu-aldimine bound in AT-ωTA, purple: docked acetophenone-aldimine in AT-ωTA. B: Position of lysine relative to PLP in fold I (<i>S</i>)-ω-transaminases: in PD-ωTA from <i>Paracoccus denitrificans</i> (4GRX, light green), PA-ωTA from <i>Pseudomonas aeruginosa</i> (4B98, turquoise) and several (<i>S</i>)-TAs identified from the Pdb by Steffen-Munsberg: from <i>Pseudomonas putida</i> (3A8U, pink), from <i>Mesorhizobium loti</i> (3GJU, yellow) and from <i>Silicobacter pomeroyi</i> (3HMU, brownish), in PD-ωTA the substrate, 5-aminopentanoate, is depicted in light green. The figures were prepared using the program PyMOL.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "iv"], "article_id"=>919550, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_fold_IV_and_fold_I_transaminases_/919550", "title"=>"Comparison of fold IV and fold I transaminases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1368347"], "description"=>"<p>Schematic drawing of the localisation of the large and small binding pocket in AT-ωTA relative to PO<sub>4</sub> and O3’ of PLP and the binding of the substrates’ substituents.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymes", "Enzyme classes", "transferases", "Enzyme structure", "proteins", "protein structure", "Recombinant proteins", "biocatalysis", "cofactors", "genetics", "Genetic mutation", "mutagenesis", "proteomics", "Protein engineering", "Computer modeling", "crystallography", "localisation", "binding", "plp"], "article_id"=>919551, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Andrzej Łyskowski", "Christian Gruber", "Georg Steinkellner", "Martin Schürmann", "Helmut Schwab", "Karl Gruber", "Kerstin Steiner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087350.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_drawing_of_the_localisation_of_the_large_and_small_binding_pocket_in_AT_TA_relative_to_PO_4_and_O3_8217_of_PLP_and_the_binding_of_the_substrates_8217_substituents_/919551", "title"=>"Schematic drawing of the localisation of the large and small binding pocket in AT-ωTA relative to PO<sub>4</sub> and O3’ of PLP and the binding of the substrates’ substituents.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-30 03:54:05"}

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Relative Metric

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