6EKX

Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with 1-naphthol (I)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

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This is version 1.3 of the entry. See complete history. 


Literature

Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase.

Ramirez-Escudero, M., Molina-Espeja, P., Gomez de Santos, P., Hofrichter, M., Sanz-Aparicio, J., Alcalde, M.

(2018) ACS Chem Biol 13: 3259-3268

  • DOI: https://doi.org/10.1021/acschembio.8b00500
  • Primary Citation of Related Structures:  
    5OXT, 5OXU, 5OY1, 5OY2, 6EKW, 6EKX, 6EKY, 6EKZ, 6EL0, 6EL4

  • PubMed Abstract: 

    • Because of their minimal requirements, substrate promiscuity and product selectivity, fungal peroxygenases are now considered to be the jewel in the crown of C-H oxyfunctionalization biocatalysts. In this work, the crystal structure of the first laboratory-evolved peroxygenase expressed by yeast was determined at a resolution of 1 ...

    Because of their minimal requirements, substrate promiscuity and product selectivity, fungal peroxygenases are now considered to be the jewel in the crown of C-H oxyfunctionalization biocatalysts. In this work, the crystal structure of the first laboratory-evolved peroxygenase expressed by yeast was determined at a resolution of 1.5 Å. Notable differences were detected between the evolved and native peroxygenase from Agrocybe aegerita, including the presence of a full N-terminus and a broader heme access channel due to the mutations that accumulated through directed evolution. Further mutagenesis and soaking experiments with a palette of peroxygenative and peroxidative substrates suggested dynamic trafficking through the heme channel as the main driving force for the exceptional substrate promiscuity of peroxygenase. Accordingly, this study provides the first structural evidence at an atomic level regarding the mode of substrate binding for this versatile biocatalyst, which is discussed within a biological and chemical context.

    Organizational Affiliation: 

    Department of Biocatalysis, Institute of Catalysis , CSIC , 28049 Madrid , Spain.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aromatic peroxygenase328Cyclocybe aegeritaMutation(s): 5 
Gene Names: APO1
EC: 1.11.2.1
UniProt
Find proteins for B9W4V6 (Cyclocybe aegerita)
Explore B9W4V6 
Go to UniProtKB:  B9W4V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9W4V6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
1NP
Query on 1NP
Download Ideal Coordinates CCD File 
N [auth A],
O [auth A]		1-NAPHTHOL
C10 H8 O
KJCVRFUGPWSIIH-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
J [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
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K [auth A],
L [auth A],
M [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MOH
Query on MOH
Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.086α = 90
b = 57.799β = 109.89
c = 60.691γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary