7PNA | pdb_00007pna

Evolved unspecific peroxygenase with A77L mutation in complex with 12-methoxylauric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.196 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PNA

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 38.1 kDa 
  • Atom Count: 2,820 
  • Modeled Residue Count: 325 
  • Deposited Residue Count: 328 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: 5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 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
7UT
(Subject of Investigation/LOI)

Query on 7UT



Download:Ideal Coordinates CCD File
K [auth A]12-methoxylauric acid
C13 H26 O3
OGLQEYICTWWJQB-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
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
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.196 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.466α = 90
b = 58.082β = 109.93
c = 61.198γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
  • Version 1.4: 2024-11-13
    Changes: Structure summary