title: Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
abstract: BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).
authors.affiliation: Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.
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authors.lastname: Grzechnik
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authors.lastname: Nigoghossian
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authors.lastname: van den Bedem
authors.forename: Dana
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authors.lastname: Weekes
authors.forename: Aprilfawn
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authors.forename: Qingping
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authors.forename: Keith O
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authors.lastname: Hodgson
authors.forename: John
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authors.lastname: Wooley
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authors.lastname: Deacon
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authors.lastname: Godzik
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authors.lastname: Wilson
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000502:physiology; D001439:Bacteroides / Q000201:enzymology; D020134:Catalytic Domain; D004396:Coloring Agents / Q000378:metabolism*; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D006418:Heme / Q000378:metabolism*; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000502:physiology; D010544:Peroxidases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020592:Shewanella / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D004396:Coloring Agents; D009097:Multienzyme Complexes; C076398:TyrA protein, Bacteria; D006418:Heme; D010544:Peroxidases