7OO5
Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades
Summary for 7OO5
| Entry DOI | 10.2210/pdb7oo5/pdb |
| Descriptor | lignin peroxidase, PROTOPORPHYRIN IX CONTAINING FE, CALCIUM ION, ... (5 entities in total) |
| Functional Keywords | ligninolytic peroxidase, plant cell-wall degrading enzyme, oxidoreductase |
| Biological source | Agrocybe pediades |
| Total number of polymer chains | 1 |
| Total formula weight | 35127.95 |
| Authors | Romero, A.,Ruiz-Duenas, F.J. (deposition date: 2021-05-26, release date: 2021-10-13, Last modification date: 2024-11-06) |
| Primary citation | Sanchez-Ruiz, M.I.,Ayuso-Fernandez, I.,Rencoret, J.,Gonzalez-Ramirez, A.M.,Linde, D.,Davo-Siguero, I.,Romero, A.,Gutierrez, A.,Martinez, A.T.,Ruiz-Duenas, F.J. Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities. Antioxidants, 10:-, 2021 Cited by PubMed Abstract: Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom . X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by HO, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds. PubMed: 34573078DOI: 10.3390/antiox10091446 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
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