8RNJ | pdb_00008rnj

Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.198 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.167 (Depositor) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural Insights and Reaction Profile of a New Unspecific Peroxygenase from Marasmius wettsteinii Produced in a Tandem-Yeast Expression System.

Sanchez-Moreno, I.Fernandez-Garcia, A.Mateljak, I.Gomez de Santos, P.Hofrichter, M.Kellner, H.Sanz-Aparicio, J.Alcalde, M.

(2024) ACS Chem Biol 19: 2240-2253

  • DOI: https://doi.org/10.1021/acschembio.4c00504
  • Primary Citation Related Structures: 
    8RNJ, 8RNK, 8RNL, 8RNM, 8RNN, 8RNO, 8RNP, 8RNQ, 8RNR

  • PubMed Abstract: 

    Fungal unspecific peroxygenases (UPOs) are gaining momentum in synthetic chemistry. Of special interest is the UPO from Marasmius rotula ( Mro UPO), which shows an exclusive repertoire of oxyfunctionalizations, including the terminal hydroxylation of alkanes, the α-oxidation of fatty acids and the C-C cleavage of corticosteroids. However, the lack of heterologous expression systems to perform directed evolution has impeded its engineering for practical applications. Here, we introduce a close ortholog of Mro UPO, a UPO gene from Marasmius wettsteinii ( Mwe UPO-1), that has a similar reaction profile to Mro UPO and for which we have set up a directed evolution platform based on tandem-yeast expression. Recombinant Mwe UPO-1 was produced at high titers in the bioreactor (0.7 g/L) and characterized at the biochemical and atomic levels. The conjunction of soaking crystallographic experiments at a resolution up to 1.6 Å together with the analysis of reaction patterns sheds light on the substrate preferences of this promiscuous biocatalyst.


  • Organizational Affiliation
    • Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 54.96 kDa 
  • Atom Count: 4,322 
  • Modeled Residue Count: 480 
  • Deposited Residue Count: 480 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Unspecific peroxygenase
A, B
240Marasmius wettsteiniiMutation(s): 0 
EC: 1.11.2.1

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
F [auth A],
N [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A],
H [auth A],
M [auth B],
O [auth B],
R [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
Q [auth B],
S [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
I [auth A],
J [auth A],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.198 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.167 (Depositor) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.574α = 90
b = 73.574β = 90
c = 186.671γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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 UniversitiesSpainSynergy CAM Project Y2018/BIO-4738-EVOQUIMERA-CM

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references