3JY1

Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.754 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 

wwPDB Validation  3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An unprecedented nucleic acid capture mechanism for excision of DNA damage.

Rubinson, E.H.Gowda, A.S.Spratt, T.E.Gold, B.Eichman, B.F.

(2010) Nature 468: 406-411

  • DOI: 10.1038/nature09428
  • Primary Citation of Related Structures:  3JX7, 3JXY, 3JXZ

  • PubMed Abstract: 
  • DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-tar ...

    DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.


    Organizational Affiliation

    Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
Molecule Chains Sequence Length Organism Details
alkylpurine DNA glycosylase AlkD
A
226 Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) N/A
Find proteins for Q816E8 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Go to UniProtKB:  Q816E8
Entity ID: 2
Molecule Chains Length Organism
DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3') B 10 N/A
Entity ID: 3
Molecule Chains Length Organism
DNA (5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*CP*C)-3') C 10 N/A
Small Molecules
Modified Residues  1 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
B
DNA LINKING C5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.754 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å) Angle (°)
a = 52.125 α = 90.00
b = 57.493 β = 101.67
c = 54.069 γ = 90.00
Software Package:
Software Name Purpose
HKL-2000 data scaling
PHASER phasing
HKL-2000 data reduction
MAR345dtb data collection
PHENIX refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance