7O1Z | pdb_00007o1z

Unspecific peroxygenase from Hypoxylon sp. EC38 in complex with S-1,2-propanediol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.168 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.123 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 
    0.124 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7O1Z

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural and biochemical studies enlighten the unspecific peroxygenase from Hypoxylon sp. EC38 as an efficient oxidative biocatalyst.

Rotilio, L.Swoboda, A.Ebner, K.Rinnofner, C.Glieder, A.Kroutil, W.Mattevi, A.

(2021) ACS Catal 11: 11511-11525

  • DOI: https://doi.org/10.1021/acscatal.1c03065
  • Primary Citation Related Structures: 
    7O1R, 7O1X, 7O1Z, 7O2D, 7O2G

  • PubMed Abstract: 

    Unspecific peroxygenases (UPO) are glycosylated fungal enzymes that can selectively oxidize C-H bonds. UPOs employ hydrogen peroxide as oxygen donor and reductant. With such an easy-to-handle co-substrate and without the need of a reducing agent, UPOs are emerging as convenient oxidative biocatalysts. Here, an unspecific peroxygenase from Hypoxylon sp. EC38 ( Hsp UPO) was identified in an activity-based screen of six putative peroxygenase enzymes that were heterologously expressed in Pichia pastoris . The enzyme was found to tolerate selected organic solvents such as acetonitrile and acetone. Hsp UPO is a versatile catalyst performing various reactions, such as the oxidation of prim - and sec -alcohols, epoxidations and hydroxylations. Semi-preparative biotransformations were demonstrated for the non-enantioselective oxidation of racemic 1-phenylethanol rac -1b (TON = 13000), giving the product with 88% isolated yield, and the oxidation of indole 6a to give indigo 6b (TON = 2800) with 98% isolated yield. Hsp UPO features a compact and rigid three-dimensional conformation that wraps around the heme and defines a funnel-shaped tunnel that leads to the heme iron from the protein surface. The tunnel extends along a distance of about 12 Å with a fairly constant diameter in its innermost segment. Its surface comprises both hydrophobic and hydrophilic groups for dealing with small-to-medium size substrates of variable polarities. The structural investigation of several protein-ligand complexes revealed that the active site of Hsp UPO is accessible to molecules of varying bulkiness and polarity with minimal or no conformational changes, explaining the relatively broad substrate scope of the enzyme. With its convenient expression system, robust operational properties, relatively small size, well-defined structural features, and diverse reaction scope, Hsp UPO is an exploitable candidate for peroxygenase-based biocatalysis.


  • Organizational Affiliation
    • Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy.

Macromolecule Content 

  • Total Structure Weight: 30.04 kDa 
  • Atom Count: 2,104 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 261 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxygenase261Hypoxylon sp. EC38Mutation(s): 0 
Gene Names: K449DRAFT_467810
EC: 1.11.2.1
UniProt
Find proteins for A0ACD6BA37 (Hypoxylon sp. (strain EC38))
Explore A0ACD6BA37 
Go to UniProtKB:  A0ACD6BA37
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BA37
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / 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
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BCN

Query on BCN



Download:Ideal Coordinates CCD File
I [auth A]BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGO
(Subject of Investigation/LOI)

Query on PGO



Download:Ideal Coordinates CCD File
C [auth A]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
1BO

Query on 1BO



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
1-BUTANOL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.168 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.123 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 0.124 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.468α = 90
b = 71.468β = 90
c = 152.655γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary