Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Journal Article · Mon Nov 22 04:00:00 EST 2010 · J. Biol. Chem.

DOI:https://doi.org/10.1074/jbc.M110.155663· OSTI ID:1014562

Bowman, Brian R; Lee, Seongmin; Wang, Shuyu; Verdine, Gregory L ^[1]

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1. Harvard University

Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction between these proteins and undamaged DNA. Here we report the crystal structures of the DNA glycosylase AlkA in complex with undamaged DNA. The structures revealed a recognition mode in which the DNA is nearly straight, with no amino acid side chains inserted into the duplex, and the target base pair is fully intrahelical. A comparison of the present structures with that of AlkA recognizing an extrahelical lesion revealed conformational changes in both the DNA and protein as the glycosylase transitions from the interrogation of undamaged DNA to catalysis of nucleobase excision. Modeling studies with the cytotoxic lesion 3-methyladenine and accompanying biochemical experiments suggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence of lesions.

• Research Organization: ANL (Argonne National Laboratory (ANL), Argonne, IL (United States)); Advanced Photon Source (APS)
• Sponsoring Organization: USDOE Office of Science (SC)
• OSTI ID: 1014562
• Journal Information: J. Biol. Chem., Journal Name: J. Biol. Chem. Journal Issue: 46 Vol. 285; ISSN JBCHA3; ISSN 0021-9258
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
AMINO ACIDS
CATALYSIS
CHAINS
CONFORMATIONAL CHANGES
CRYSTAL STRUCTURE
DNA
DNA DAMAGES
ESCHERICHIA COLI
PROTEINS
SIMULATION
TARGETS