7d8m | pdb_00007d8m

Crystal structure of DyP

spinqualitylabelsall models 7d8m, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7d8m is a 1 chain structure with sequence from Irpex lacteus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2Å Ligands: HEM, OXY Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A2P1C6N4_IRPLA Publication Abstract from PubMed BACKGROUND: Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H2O2 as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood. RESULTS: Here, we obtained a high-resolution structure (2.0 A, PDB: 7D8M) of IlDyP4 with alpha-helices, anti-parallel beta-sheets and one ferric heme cofactor sandwiched between two domains. The crystal structure of IlDyP4 revealed two heme access channels leading from the enzyme molecular surface to its heme region, and also showed four conserved amino acid residues forming the pocket for the conversion of hydrogen peroxide into the water molecule. In addition, we found that Trp264 and Trp380, were two important residues with different roles in IlDyP4, by using site-directed mutagenesis and an electron paramagnetic resonance (EPR) study. Trp264 is a noncatalytic residue that mainly is used for maintaining the normal spatial conformation of the heme region and the high-spin state of heme Fe(3+) of IlDyP4, while Trp380 serves as the surface-exposed radical-forming residue that is closely related to the oxidation of substrates including not only bulky dyes, but also simple phenols. CONCLUSIONS: This study is important for better understanding the catalytic properties of fungal DyPs and their structure-function relationships. Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17.,Li L, Wang T, Chen T, Huang W, Zhang Y, Jia R, He C Biotechnol Biofuels. 2021 May 31;14(1):128. doi: 10.1186/s13068-021-01978-y. PMID:34059116 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Proteopedia Page Contributors and Editors (what is this?)

OCA