7OO5 | pdb_00007oo5

Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades

• PDB DOI: https://doi.org/10.2210/pdb7OO5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Agrocybe pediades
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-26 Released: 2021-10-13 
• Deposition Author(s): Romero, A., Ruiz-Duenas, F.J.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.269 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities.

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.

(2021) Antioxidants (Basel) 10

• PubMed: 34573078 
• DOI: https://doi.org/10.3390/antiox10091446
• Primary Citation Related Structures: 
  7OO5


• 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 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 H ₂ O ₂ , 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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Organizational Affiliation: 
• Centro de Investigaciones Biológicas "Margarita Salas" (CIB), Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas (CSIC), 41012 Seville, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.13 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 331 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lignin peroxidase	A	331	Agrocybe pediades	Mutation(s): 0  EC: 1.11.1.14 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for A0A8X6EH08 (Agrocybe pediades) Explore A0A8X6EH08  Go to UniProtKB:  A0A8X6EH08

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.269 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.126	α = 90
b = 74.95	β = 90
c = 82.768	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Romero, A., Ruiz-Duenas, F.J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2016-77835-R

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary