2HVI

ddCTP:G pair in the polymerase active site (0 position)

Summary for 2HVI

• Entry DOI: 10.2210/pdb2hvi/pdb
• Related: 1LV5 2HHQ 2HHS 2HHT 2HHU 2HHV 2HHW 2HHX 2HHY 2HVH 2HW3
• Related PRD ID: PRD_900003
• Descriptor: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3', 5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', DNA Polymerase I, ... (8 entities in total)
• Functional Keywords: dna polymerase i, dna replication, klenow fragment, protein-dna complex, closed conformation, transferase-dna complex, transferase/dna
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 6
• Total formula weight: 147973.43

Authors

Warren, J.J.,Forsberg, L.J.,Beese, L.S. (deposition date: 2006-07-28, release date: 2006-12-12, Last modification date: 2023-08-30)

Primary citation

Warren, J.J.,Forsberg, L.J.,Beese, L.S.
The structural basis for the mutagenicity of O6-methyl-guanine lesions.
Proc.Natl.Acad.Sci.Usa, 103:19701-19706, 2006

PubMed Abstract: Methylating agents are widespread environmental carcinogens that generate a broad spectrum of DNA damage. Methylation at the guanine O(6) position confers the greatest mutagenic and carcinogenic potential. DNA polymerases insert cytosine and thymine with similar efficiency opposite O(6)-methyl-guanine (O6MeG). We combined pre-steady-state kinetic analysis and a series of nine x-ray crystal structures to contrast the reaction pathways of accurate and mutagenic replication of O6MeG in a high-fidelity DNA polymerase from Bacillus stearothermophilus. Polymerases achieve substrate specificity by selecting for nucleotides with shape and hydrogen-bonding patterns that complement a canonical DNA template. Our structures reveal that both thymine and cytosine O6MeG base pairs evade proofreading by mimicking the essential molecular features of canonical substrates. The steric mimicry depends on stabilization of a rare cytosine tautomer in C.O6MeG-polymerase complexes. An unusual electrostatic interaction between O-methyl protons and a thymine carbonyl oxygen helps stabilize T.O6MeG pairs bound to DNA polymerase. Because DNA methylators constitute an important class of chemotherapeutic agents, the molecular mechanisms of replication of these DNA lesions are important for our understanding of both the genesis and treatment of cancer.

PubMed: 17179038
DOI: 10.1073/pnas.0609580103

Experimental method

X-RAY DIFFRACTION (1.98 Å)