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Báo cáo khoa học: The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue

The dye-decolorizing peroxidase (DyP)-type peroxidase family is a unique heme peroxidase family. The primary and tertiary structures of this family are obviously different from those of other heme peroxidases. However, the details of the structure–function relationships of this family remain poorly understood. | IFEBS Journal The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue Toru Yoshida1 Hideaki Tsuge2 Hiroki Konno1 Toru Hisabori1 and Yasushi Sugano1 1 R1-7 ChemicalResources Laboratory Tokyo Institute of Technology Japan 2 Department of Bioresources and EnvironmentalSciences Kyoto Sangyo University Japan Keywords catalytic mechanism DyP DyP-type peroxidase heme protein swing mechanism Correspondence Y. Sugano R1-7 ChemicalResources Laboratory Tokyo Institute of Technology 4259 Nagatsuta Midori-ku Yokohama 226-8503 Japan Fax 81 45 924 5268 Tel 81 45 924 5235 E-mail ysugano@res.titech.ac.jp Received 23 February 2011 revised 1 April 2011 accepted 4 May 2011 doi 10.1111 j.1742-4658.2011.08161.x The dye-decolorizing peroxidase DyP -type peroxidase family is a unique heme peroxidase family. The primary and tertiary structures of this family are obviously different from those of other heme peroxidases. However the details of the structure-function relationships of this family remain poorly understood. We show four high-resolution structures of DyP EC 1.11.1.19 which is representative of this family the native DyP 1.40 A the D171N mutant DyP 1.42 A the native DyP complexed with cyanide 1.45 A and the D171N mutant DyP associated with cyanide 1.40 A . These structures contain four amino acids forming the binding pocket for hydrogen peroxide and they are remarkably conserved in this family. Moreover these structures show that OD2 of Asp171 accepts a proton from hydrogen peroxide in compound I formation and that OD2 can swing to the appropriate position in response to the ligand for heme iron. On the basis of these results we propose a swing mechanism in compound I formation. When DyP reacts with hydrogen peroxide OD2 swings towards an optimal position to accept the proton from hydrogen peroxide bound to the heme iron. Introduction Heme peroxidase one of the best-studied and most ubiquitous enzymes oxidizes a .