5DAV

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with 4-Methoxydehydrocyclopeptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the Dioxygenase AsqJ: Mechanistic Insights into a One-Pot Multistep Quinolone Antibiotic Biosynthesis.

Brauer, A.Beck, P.Hintermann, L.Groll, M.

(2016) Angew Chem Int Ed Engl 55: 422-426

  • DOI: https://doi.org/10.1002/anie.201507835
  • Primary Citation of Related Structures:  
    5DAP, 5DAQ, 5DAV, 5DAW, 5DAX

  • PubMed Abstract: 

    Multienzymatic cascades are responsible for the biosynthesis of natural products and represent a source of inspiration for synthetic chemists. The Fe(II)/α-ketoglutarate-dependent dioxygenase AsqJ from Aspergillus nidulans is outstanding because it stereoselectively catalyzes both a ferryl-induced desaturation reaction and epoxidation on a benzodiazepinedione. Interestingly, the enzymatically formed spiro epoxide spring-loads the 6,7-bicyclic skeleton for non-enzymatic rearrangement into the 6,6-bicyclic scaffold of the quinolone alkaloid 4'-methoxyviridicatin. Herein, we report different crystal structures of the protein in the absence and presence of synthesized substrates, surrogates, and intermediates that mimic the various stages of the reaction cycle of this exceptional dioxygenase.


  • Organizational Affiliation

    Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching (Germany).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230)308Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: AN9227.2ANIA_09227
EC: 1.14.11.81
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
58J
Query on 58J

Download Ideal Coordinates CCD File 
C [auth A]4-Methoxydehydrocyclopeptin
C18 H16 N2 O3
MWFWGXGLRBDFOQ-WJDWOHSUSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
BR
Query on BR

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.05α = 90
b = 120.77β = 90
c = 66.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB749

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description