Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 140.42 kDa 
• Atom Count: 9845 
• Modelled Residue Count: 1174 
• Deposited Residue Count: 1176 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3D4V

Crystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:Cytosine Base Pair

• DOI: 10.2210/pdb3D4V/pdb
• NDB: PD1147

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-15 Released: 2008-09-09 
• Deposition Author(s): Lee, S., Bowman, B.R., Wang, S., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.208 

Literature

Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.

Lee, S., Bowman, B.R., Ueno, Y., Wang, S., Verdine, G.L.

(2008) J Am Chem Soc 130: 11570-11571

• PubMed: 18686953 
• DOI: 10.1021/ja8025328
• Primary Citation of Related Structures:  
  3D4V


• PubMed Abstract: 
  

The predominant product of aberrant DNA methylation is the genotoxic lesion N7-methyl-2'-deoxyguanosine (m7dG). M7dG is recognized and excised by lesion-specific DNA glycosylases, namely AlkA in E. coli and Aag in humans. Structural studies of m7dG recognition and catalysis by these enzymes have been hampered due to a lack of efficient means by which to incorporate the chemically labile m7dG moiety site-specifically into DNA on a preparative scale. Here we report a solution to this problem. We stabilized the lesion toward acid-catalyzed and glycosylase-catalyzed depurination by 2'-fluorination and toward base-catalyzed degradation using mild, nonaqueous conditions in the DNA deprotection reaction. Duplex DNA containing 2'-fluoro-m7dG (Fm7dG) cocrystallized with AlkA as a host-guest complex in which the lesion-containing segment of DNA was nearly devoid of protein contacts, thus enabling the first direct visualization of the N7-methylguanine lesion nucleobase in DNA. The structure reveals that the base-pairing mode of Fm7dG:C is nearly identical to that of G:C, and Fm7dG does not induce any apparent structural disturbance of the duplex structure. These observations suggest that AlkA and Aag must perform a structurally invasive interrogation of DNA in order to detect the presence of intrahelical m7dG lesions.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-3-methyladenine glycosylase 2	A, B, C, D	282	Escherichia coli	Mutation(s): 0  Gene Names: alkA, aidA, b2068, JW2053 EC: 3.2.2.21
Find proteins for P04395 (Escherichia coli (strain K12)) Explore P04395  Go to UniProtKB:  P04395

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3'	E, G	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3'	F, H	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.1	α = 90
b = 100.361	β = 94.45
c = 102.281	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-15 
• Released Date: 2008-09-09 
Deposition Author(s): Lee, S., Bowman, B.R., Wang, S., Verdine, G.L.

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description