5VJ0
Crystal Structure of heme-containing DyP Type Peroxidase from Enterobacter lignolyticus
Summary for 5VJ0
| Entry DOI | 10.2210/pdb5vj0/pdb |
| Descriptor | Dyp-type peroxidase family, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total) |
| Functional Keywords | enterobacter lignolyticus, peroxidase, heme, lignin, oxidoreductase |
| Biological source | Enterobacter lignolyticus |
| Total number of polymer chains | 4 |
| Total formula weight | 144149.03 |
| Authors | Meekins, D.A.,Li, P.,Geisbrecht, B.V. (deposition date: 2017-04-17, release date: 2017-08-16, Last modification date: 2023-10-04) |
| Primary citation | Shrestha, R.,Huang, G.,Meekins, D.A.,Geisbrecht, B.V.,Li, P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal, 7:6352-6364, 2017 Cited by PubMed Abstract: Dye-decolorizing peroxidases (DyPs) are a family of HO-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class DyP from . Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type DyP with DO at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of / and suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-DyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity. PubMed: 29308295DOI: 10.1021/acscatal.7b01861 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.93 Å) |
Structure validation
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