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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nature06889
  • Primary Citation of Related Structures:  3BI3, 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 doub ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-ketoglutarate-dependent dioxygenase alkB
A
202Escherichia coli (strain K12)Gene Names: alkB (aidD)
EC: 1.14.11.33
Find proteins for P05050 (Escherichia coli (strain K12))
Go to UniProtKB:  P05050
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7)P*DAP*DCP*DCP*DGP*DT)-3')B12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3')C13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MA7
Query on MA7
B
DNA LINKINGC11 H17 N5 O6 PDA
2YR
Query on 2YR
B
NON-POLYMERC11 H18 N3 O7 P S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.413α = 90.00
b = 75.822β = 108.53
c = 52.228γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASESphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-11-30 
  • Released Date: 2008-04-22 
  • Deposition Author(s): Yi, C., Yang, C.-G.

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-05-28
    Type: Non-polymer description, Structure summary