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The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions [electronic resource].

Published
Washington, D.C. : United States. Dept. of Energy. Office of Science, 2015.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy
Physical Description
pages 254-258 : digital, PDF file
Additional Creators
United States. Department of Energy. Office of Science, National Science Foundation (U.S.), National Institutes of Health (U.S.), and United States. Department of Energy. Office of Scientific and Technical Information
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Summary
Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. In this paper, we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge–dipole and CH–π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Finally and hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.
Report Numbers
E 1.99:1229895
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Note
Published through SciTech Connect.
10/28/2015.
Nature (London) 527 7577 ISSN 0028-0836 AM
Elwood A. Mullins; Rongxin Shi; Zachary D. Parsons; Philip K. Yuen; Sheila S. David; Yasuhiro Igarashi; Brandt F. Eichman.
Vanderbilt Univ., Nashville, TN (United States)
Michigan Economic Development Corporation (United States)
Michigan Technology Tri-Corridor (United States)
Vanderbilt Univ. (United States)
Funding Information
AC02-06CH11357
MCB-1122098
MCB-1517695
R01ES019625
R01CA067985
S10RR026915
085P1000817
T32ES07028
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