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Review
. 2013 Jan 1;5(1):a012575.
doi: 10.1101/cshperspect.a012575.

DNA Repair by Reversal of DNA Damage

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Free PMC article
Review

DNA Repair by Reversal of DNA Damage

Chengqi Yi et al. Cold Spring Harb Perspect Biol. .
Free PMC article

Erratum in

  • Cold Spring Harb Perspect Biol. 2014 Apr;6(4):a023440

Abstract

Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology.

Figures

Figure 1.
Figure 1.
Direct DNA-repair pathways: representative substrates, repair proteins and cofactors, and corresponding repair products.
Figure 2.
Figure 2.
Mechanisms and structures of representative photolyases from different classes. (A) Mechanisms of photorepair for CPD photolyases. The generation of fully reduced, active FADH* species is different for Class I and Class II CPD photolyases. (B) Repair mechanism of (6–4) photolyases. (C) Representative complex structures of photolyases bound to double-stranded DNA (dsDNA) (PDB accession code: 1TEZ, 2XRZ, and 3CVU).
Figure 3.
Figure 3.
Overall structures and damage-binding pockets of hAGT and Schizosaccharomyces pombe Atl1. (A) Structures of hAGT/DNA bound to a 6-meG (1T38), an N4-p-xylylenediamine cytosine, and a partially flipped thymine (1YFH). (B) Active site of hAGT C145S with a bound 6-meG. (C) Overall and binding-site structure of Atl1 (3GYH).
Figure 4.
Figure 4.
Structure and mechanism of AlkB-mediated oxidative demethylation. (A) Structure of AlkB/d(T-1meA-T) (2FD8). (B) Structure of overall AlkB/DNA complex and the active site (3BIE). (C) Direct observation of oxidative-demethylation intermediates in crystallo.
Figure 5.
Figure 5.
Structures and functions of AlkB homologs. (A) Structures of ALKBH2 with a bound 1-meA (3BTY) and a central C:G base pair (3RZG), which the protein is interrogating. (B) Structure of ALKBH3(2IUW). (C) Structure of FTO (3LFM). (D) ALKBH8 is a transfer RNA (tRNA) modification enzyme. (E) Demethylation of 6-meA by FTO enables reversible RNA modification.

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