3BIE

X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA

Yang, C.-G.Yi, C.Duguid, E.M.Sullivan, C.T.Jian, X.Rice, P.A.He, C.

(2008) Nature 452: 961-965

  • DOI: https://doi.org/10.1038/nature06889
  • Primary Citation of Related Structures:  
    3BI3, 3BIE, 3BKZ, 3BTX, 3BTY, 3BTZ, 3BU0, 3BUC

  • PubMed Abstract: 

    Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.


  • Organizational Affiliation

    Department of Chemistry, 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 alkB202Escherichia coli K-12Mutation(s): 1 
Gene Names: alkbaidd
EC: 1.14.11 (PDB Primary Data), 1.14.11.33 (UniProt)
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(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7)P*DAP*DCP*DCP*DGP*DT)-3')12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3')13N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.413α = 90
b = 75.822β = 108.53
c = 52.228γ = 90
Software Package:
Software NamePurpose
PHASESphasing
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: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-05-28
    Changes: Non-polymer description, Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary