7PN8

Evolved unspecific peroxygenase with A77L mutation in complex with tetradecane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids.

Gomez de Santos, P.Gonzalez-Benjumea, A.Fernandez-Garcia, A.Aranda, C.Wu, Y.But, A.Molina-Espeja, P.Mate, D.M.Gonzalez-Perez, D.Zhang, W.Kiebist, J.Scheibner, K.Hofrichter, M.Swiderek, K.Moliner, V.Sanz-Aparicio, J.Hollmann, F.Gutierrez, A.Alcalde, M.

(2023) Angew Chem Int Ed Engl 62: e202217372-e202217372

  • DOI: https://doi.org/10.1002/anie.202217372
  • Primary Citation of Related Structures:  
    7PN4, 7PN5, 7PN6, 7PN7, 7PN8, 7PN9, 7PNA

  • PubMed Abstract: 

    The hydroxylation of fatty acids is an appealing reaction in synthetic chemistry, although the lack of selective catalysts hampers its industrial implementation. In this study, we have engineered a highly regioselective fungal peroxygenase for the ω-1 hydroxylation of fatty acids with quenched stepwise over-oxidation. One single mutation near the Phe catalytic tripod narrowed the heme cavity, promoting a dramatic shift toward subterminal hydroxylation with a drop in the over-oxidation activity. While crystallographic soaking experiments and molecular dynamic simulations shed light on this unique oxidation pattern, the selective biocatalyst was produced by Pichia pastoris at 0.4 g L -1 in a fed-batch bioreactor and used in the preparative synthesis of 1.4 g of (ω-1)-hydroxytetradecanoic acid with 95 % regioselectivity and 83 % ee for the S enantiomer.


  • Organizational Affiliation

    Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, 41012, Seville, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic peroxygenase328Cyclocybe aegeritaMutation(s): 6 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG
Query on NAG

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F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
C14 (Subject of Investigation/LOI)
Query on C14

Download Ideal Coordinates CCD File 
K [auth A]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
PO4
Query on PO4

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B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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L [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

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D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.172α = 90
b = 57.996β = 110.08
c = 60.863γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainComunidad de Madrid Synergy CAM project Y2018/BIO-4738-EVOCHIMERA-CM

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-03-01
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description