2YOR

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits

Piontek, K.Strittmatter, E.Ullrich, R.Grobe, G.Pecyna, M.J.Kluge, M.Scheibner, K.Hofrichter, M.Plattner, D.A.

(2013) J.Biol.Chem. 288: 34767

  • DOI: 10.1074/jbc.M113.514521
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunction ...

    Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio- and stereoselectivities. When compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons. Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO.


    Related Citations: 
    • Crystallization of a 45 kDa Peroxygenase/Peroxidase from the Mushroom Agrocybe Aegerita and Structure Determination by Sad Utilizing Only the Haem Iron.
      Piontek, K.,Ullrich, R.,Liers, C.,Diederichs, K.,Plattner, D.A.,Hofrichter, M.
      (2010) Acta Crystallogr.,Sect.F 66: 693


    Organizational Affiliation

    From the Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AROMATIC PEROXYGENASE
A, B
325Agrocybe aegeritaMutation(s): 0 
Gene Names: APO1
EC: 1.11.2.1
Find proteins for B9W4V6 (Agrocybe aegerita)
Go to UniProtKB:  B9W4V6
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MZ0
Query on MZ0

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A, B
1H-imidazol-5-ylmethanol
4(5)-(hydroxymethyl)imidazole
C4 H6 N2 O
QDYTUZCWBJRHKK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.290α = 90.00
b = 95.030β = 90.00
c = 127.200γ = 90.00
Software Package:
Software NamePurpose
SOLOMONphasing
autoSHARPphasing
SHELXDphasing
XDSdata scaling
REFMACrefinement
SOLOMONmodel building
SHELXEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2015-04-01
    Type: Database references