7OLK

Dioxygenase AsqJ in complex with 2b and Tris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ.

Auman, D.Ecker, F.Mader, S.L.Dorst, K.M.Brauer, A.Widmalm, G.Groll, M.Kaila, V.R.I.

(2022) J Am Chem Soc 144: 15622-15632

  • DOI: https://doi.org/10.1021/jacs.2c05650
  • Primary Citation of Related Structures:  
    7OLK, 7OLL, 7OLM, 7OLO, 7OLP, 7OLQ, 7OLR, 7OLT

  • PubMed Abstract: 

    Dioxygenases catalyze stereoselective oxygen atom transfer in metabolic pathways of biological, industrial, and pharmaceutical importance, but their precise chemical principles remain controversial. The α-ketoglutarate (αKG)-dependent dioxygenase AsqJ synthesizes biomedically active quinolone alkaloids via desaturation and subsequent epoxidation of a carbon-carbon bond in the cyclopeptin substrate. Here, we combine high-resolution X-ray crystallography with enzyme engineering, quantum-classical (QM/MM) simulations, and biochemical assays to describe a peroxidic intermediate that bridges the substrate and active site metal ion in AsqJ. Homolytic cleavage of this moiety during substrate epoxidation generates an activated high-valent ferryl (Fe IV = O) species that mediates the next catalytic cycle, possibly without the consumption of the metabolically valuable αKG cosubstrate. Our combined findings provide an important understanding of chemical bond activation principles in complex enzymatic reaction networks and molecular mechanisms of dioxygenases.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron/alpha-ketoglutarate-dependent dioxygenase asqJ308Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: asqJAN9227
EC: 1.14 (PDB Primary Data), 1.14.11.81 (UniProt)
UniProt
Find proteins for Q5AR53 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore Q5AR53 
Go to UniProtKB:  Q5AR53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5AR53
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO0
Query on CO0

Download Ideal Coordinates CCD File 
C [auth A](3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione
C17 H14 N2 O2
FYVKHLSOIIPVEH-PTNGSMBKSA-N
TRS (Subject of Investigation/LOI)
Query on TRS

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D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
BR (Subject of Investigation/LOI)
Query on BR

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E [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
NI (Subject of Investigation/LOI)
Query on NI

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B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.09α = 90
b = 119.95β = 90
c = 66.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description