7OO5 image
Entry Detail
PDB ID:
7OO5
Keywords:
Title:
Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2021-05-26
Release Date:
2021-10-13
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.26
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:lignin peroxidase
Chain IDs:A
Chain Length:331
Number of Molecules:1
Biological Source:Agrocybe pediades
Primary Citation

Abstact

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 Agrocybe pediades. 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 H2O2, 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.

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