6EOZ

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72K mutant in complex with cyclopeptin (1b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ.

Mader, S.L.Brauer, A.Groll, M.Kaila, V.R.I.

(2018) Nat Commun 9: 1168-1168

  • DOI: https://doi.org/10.1038/s41467-018-03442-2
  • Primary Citation of Related Structures:  
    5OA4, 5OA7, 5OA8, 6EOZ

  • PubMed Abstract: 

    The recently discovered Fe II /α-ketoglutarate-dependent dioxygenase AsqJ from Aspergillus nidulans stereoselectively catalyzes a multistep synthesis of quinolone alkaloids, natural products with significant biomedical applications. To probe molecular mechanisms of this elusive catalytic process, we combine here multi-scale quantum and classical molecular simulations with X-ray crystallography, and in vitro biochemical activity studies. We discover that methylation of the substrate is essential for the activity of AsqJ, establishing molecular strain that fine-tunes π-stacking interactions within the active site. To rationally engineer AsqJ for modified substrates, we amplify dispersive interactions within the active site. We demonstrate that the engineered enzyme has a drastically enhanced catalytic activity for non-methylated surrogates, confirming our computational data and resolved high-resolution X-ray structures at 1.55 Å resolution. Our combined findings provide crucial mechanistic understanding of the function of AsqJ and showcase how combination of computational and experimental data enables to rationally engineer enzymes.


  • Organizational Affiliation

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


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): 1 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.56α = 90
b = 120.14β = 90
c = 67.17γ = 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 FoundationGermanySFB1035

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description