6kmm | pdb_00006kmm

Crystal Structure of HEPES bound Dye Decolorizing peroxidase from Bacillus subtilis

spinqualitylabelsall models 6kmm, resolution 1.93Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.93Å Ligands: CL, EPE, GOL, HEM, MPD, NA, OXY, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The dye-decolorizing peroxidases (DyPs) belong to a unique heme peroxidase family for their biotechnological potential to detoxify synthetic dyes. In this work, we have biochemically and structurally characterized the dye-decolorizing peroxidase from Bacillus subtilis (BsDyP). The biochemical studies of BsDyP demonstrate that pH 4.0 is optimum for the oxidation of malachite green (MG) and methyl violet (MV). However, it oxidizes the MG with higher catalytic efficiency (kcat/Km = 6.3 x 10(2) M(-1)s(-1)), than MV (kcat/Km = 5.0 x 10(2) M(-1)s(-1)). While reactive black 5 (RB5) is oxidized at pH 3.0 with the catalytic efficiency of kcat/Km = 3.6 x 10(2) M(-1)s(-1). The calculated thermodynamic parameters by isothermal titration calorimetry (ITC) reveal the feasibility and spontaneity of dyes binding with BsDyP. Further, the crystal structures of a HEPES bound and unbound of BsDyP provide insight into the probable binding sites of the substrates. In BsDyP-HEPES bound structure, the HEPES-1 molecule is found in the heme cavity at the gamma-edge, and another HEPES-2 molecule is bound ~16 A away from the heme that is fenced by Ile231, Arg234, Ser235, Asp239, Glu334, and surface-exposed Tyr335 residues. Furthermore, the molecular docking, simulation, and MMPBSA studies support the binding of dyes at both the sites of BsDyP and produce lower-energy stable BsDyP-dyes complexes. Here, the BsDyP study allows the identification of its two potential binding sites and shows the oxidation of a variety of dyes. Structural and functional insight of BsDyP will facilitate its engineering for the improved decolorization of dyes. Characterization of dye-decolorizing peroxidase from Bacillus subtilis.,Dhankhar P, Dalal V, Mahto JK, Gurjar BR, Tomar S, Sharma AK, Kumar P Arch Biochem Biophys. 2020 Oct 30;693:108590. doi: 10.1016/j.abb.2020.108590., Epub 2020 Sep 21. PMID:32971035 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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