3H8X

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.

Lu, L.Yi, C.Jian, X.Zheng, G.He, C.

(2010) Nucleic Acids Res. 38: 4415-4425

  • DOI: 10.1093/nar/gkq129
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N(1)-meA and N(3)-meC are cytotoxic DNA base methylation lesions that can accumulate in the genomes of various organisms in the presence of S(N)2 type methylating agents. We report here the structural characterization of these base lesions in duplex ...

    N(1)-meA and N(3)-meC are cytotoxic DNA base methylation lesions that can accumulate in the genomes of various organisms in the presence of S(N)2 type methylating agents. We report here the structural characterization of these base lesions in duplex DNA using a cross-linked protein-DNA crystallization system. The crystal structure of N(1)-meA:T pair shows an unambiguous Hoogsteen base pair with a syn conformation adopted by N(1)-meA, which exhibits significant changes in the opening, roll and twist angles as compared to the normal A:T base pair. Unlike N(1)-meA, N(3)-meC does not establish any interaction with the opposite G, but remains partially intrahelical. Also, structurally characterized is the N(6)-meA base modification that forms a normal base pair with the opposite T in duplex DNA. Structural characterization of these base methylation modifications provides molecular level information on how they affect the overall structure of duplex DNA. In addition, the base pairs containing N(1)-meA or N(3)-meC do not share any specific characteristic properties except that both lesions create thermodynamically unstable regions in a duplex DNA, a property that may be explored by the repair proteins to locate these lesions.


    Organizational Affiliation

    Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
A
209Homo sapiensMutation(s): 4 
Gene Names: ALKBH2 (ABH2)
EC: 1.14.11.33
Find proteins for Q6NS38 (Homo sapiens)
Go to Gene View: ALKBH2
Go to UniProtKB:  Q6NS38
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*TP*(ME6)P*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3'B13synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*CP*AP*AP*TP*AP*AP*GP*AP*CP*A)-3'C13synthetic construct
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ME6
Query on ME6
B
DNA linkingC10 H17 N3 O7 PDC
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: 1.95 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.110α = 90.00
b = 79.110β = 90.00
c = 242.270γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-06-04
    Type: Other