2XO7

Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chemical Discrimination between Dc and 5Medc Via Their Hydroxylamine Adducts

Muenzel, M.Lercher, L.Mueller, M.Carell, T.

(2010) Nucleic Acids Res. 38: E192

  • DOI: 10.1093/nar/gkq724

  • PubMed Abstract: 
  • The presence of the methylated nucleobase (5Me)dC in CpG islands is a key factor that determines gene silencing. False methylation patterns are responsible for deteriorated cellular development and are a hallmark of many cancers. Today genes can be s ...

    The presence of the methylated nucleobase (5Me)dC in CpG islands is a key factor that determines gene silencing. False methylation patterns are responsible for deteriorated cellular development and are a hallmark of many cancers. Today genes can be sequenced for the content of (5Me)dC only with the help of the bisulfite reagent, which is based exclusively on chemical reactivity differences established by the additional methyl group. Despite intensive optimization of the bisulfite protocol, the method still has specificity problems. Most importantly ∼95% of the DNA analyte is degraded during the analysis procedure. We discovered that the reagent O-allylhydroxylamine is able to discriminate between dC and (5Me)dC. The reagent, in contrast to bisulfite, does not exploit reactivity differences but gives directly different reaction products. The reagent forms a stable mutagenic adduct with dC, which can exist in two states (E versus Z). In case of dC the allylhydroxylamine adduct switches into the E-isomeric form, which generates dC to dT transition mutations that can easily be detected by established methods. Significantly, the (5Me)dC-adduct adopts exclusively the Z-isomeric form, which causes the polymerase to stop. O-allylhydroxylamine does allow differentiation between dC and (5Me)dC with high accuracy, leading towards a novel and mild chemistry for methylation analysis.


    Organizational Affiliation

    Department of Chemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Butenandtstr. 5-13, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE I
A
580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Go to UniProtKB:  E1C9K5
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3'B10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3'C11synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
47C
Query on 47C
B
DNA LINKINGC12 H18 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.478α = 90.00
b = 93.636β = 90.00
c = 105.091γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-09-21
    Type: Database references, Version format compliance