3O1R

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.

Yi, C.Jia, G.Hou, G.Dai, Q.Zhang, W.Zheng, G.Jian, X.Yang, C.G.Cui, Q.He, C.

(2010) Nature 468: 330-333

  • DOI: https://doi.org/10.1038/nature09497
  • Primary Citation of Related Structures:  
    3O1M, 3O1O, 3O1P, 3O1R, 3O1S, 3O1T, 3O1U, 3O1V

  • PubMed Abstract: 

    Mononuclear iron-containing oxygenases conduct a diverse variety of oxidation functions in biology, including the oxidative demethylation of methylated nucleic acids and histones. Escherichia coli AlkB is the first such enzyme that was discovered to repair methylated nucleic acids, which are otherwise cytotoxic and/or mutagenic. AlkB human homologues are known to play pivotal roles in various processes. Here we present structural characterization of oxidation intermediates for these demethylases. Using a chemical cross-linking strategy, complexes of AlkB-double stranded DNA (dsDNA) containing 1,N(6)-etheno adenine (εA), N(3)-methyl thymine (3-meT) and N(3)-methyl cytosine (3-meC) are stabilized and crystallized, respectively. Exposing these crystals, grown under anaerobic conditions containing iron(II) and α-ketoglutarate (αKG), to dioxygen initiates oxidation in crystallo. Glycol (from εA) and hemiaminal (from 3-meT) intermediates are captured; a zwitterionic intermediate (from 3-meC) is also proposed, based on crystallographic observations and computational analysis. The observation of these unprecedented intermediates provides direct support for the oxidative demethylation mechanism for these demethylases. This study also depicts a general mechanistic view of how a methyl group is oxidatively removed from different biological substrates.


  • Organizational Affiliation

    Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase AlkB206Escherichia coli K-12Mutation(s): 1 
Gene Names: alkBaidDb2212JW2200
EC: 1.14.11
UniProt
Find proteins for P05050 (Escherichia coli (strain K12))
Explore P05050 
Go to UniProtKB:  P05050
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05050
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDK)P*AP*CP*CP*GP*T)-3')12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3')13N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.465α = 90
b = 75.83β = 108.24
c = 51.976γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2014-05-28
    Changes: Non-polymer description, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description