7PN4

Evolved unspecific peroxygenase with A77L mutation in complex with naphthalene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.209 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted NPYClick on this verticalbar to view details

This is version 1.4 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

    Evoenzyme, S.L., Parque Científico de Madrid, C/Faraday 7, 28049, Madrid, 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
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

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

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
I [auth A],
J [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NPY (Subject of Investigation/LOI)
Query on NPY

Download Ideal Coordinates CCD File 
F [auth A]NAPHTHALENE
C10 H8
UFWIBTONFRDIAS-UHFFFAOYSA-N
PO4
Query on PO4

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H [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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D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MOH
Query on MOH

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K [auth A],
M [auth A]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.957α = 90
b = 57.651β = 109.44
c = 60.628γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted NPYClick on this verticalbar to view details

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
  • Version 1.4: 2024-11-06
    Changes: Structure summary