3D4V

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

Summary for 3D4V

• Entry DOI: 10.2210/pdb3d4v/pdb
• Descriptor: DNA-3-methyladenine glycosylase 2, 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3', 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3', ... (4 entities in total)
• Functional Keywords: alka, n7methylguanine, dna repair, host-guest complex, dna structure, dna damage, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 8
• Total formula weight: 140418.59

Authors

Lee, S.,Bowman, B.R.,Wang, S.,Verdine, G.L. (deposition date: 2008-05-15, release date: 2008-09-09, Last modification date: 2024-02-21)

Primary citation

Lee, S.,Bowman, B.R.,Ueno, Y.,Wang, S.,Verdine, G.L.
Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.
J.Am.Chem.Soc., 130:11570-11571, 2008

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.

PubMed: 18686953
DOI: 10.1021/ja8025328

Experimental method

X-RAY DIFFRACTION (2.9 Å)