Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
Journal of Biological Chemistry (Impact Factor: 4.57). 04/2012; 287(30):24916-28. DOI: 10.1074/jbc.M111.316497
Source: PubMed


A poorly understood aspect of DNA repair proteins is their ability to identify exceedingly rare sites of damage embedded in a large excess of nearly identical undamaged DNA, while catalyzing repair only at the damaged sites. Progress toward understanding this problem has been made by comparing the structures and biochemical behavior of these enzymes when they are presented with either a target lesion or a corresponding undamaged nucleobase. Trapping and analyzing such DNA-protein complexes is particularly difficult in the case of base extrusion DNA repair proteins because of the complexity of the repair reaction, which involves extrusion of the target base from DNA followed by its insertion into the active site where glycosidic bond cleavage is catalyzed. Here we report the structure of a human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, in which a normal guanine from DNA has been forcibly inserted into the enzyme active site. Although the interactions of the nucleobase with the active site are only subtly different for G versus oxoG, hOGG1 fails to catalyze excision of the normal nucleobase. This study demonstrates that even if hOGG1 mistakenly inserts a normal base into its active site, the enzyme can still reject it on the basis of catalytic incompatibility.

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Available from: Gregory L Verdine, Dec 18, 2013
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    • "It thus appears that the observed dipole is not mandatory for 8-oxoG discrimination or catalysis. This observation seems to be corroborated by the structure of hOGG1 in complex with guanine (PDB ID: 3IH7 [48]) in which the guanine base occupies the exact same position as observed for 8-oxoG in the hOGG1-8oxoG DNA complex (PDB ID: 1EBM [29]). The possible contribution of the “dipole effect” on 8-oxoG binding is unlikely to occur in OGG2 or AGOG in which the residue corresponding to Cys235 in hOGG1 is a histidine in OGG2 or a phenylalanine in AGOG. "
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    ABSTRACT: Amongst the four bases that form DNA, guanine is the most susceptible to oxidation, and its oxidation product, 7,8-dihydro-8-oxoguanine (8-oxoG) is the most prevalent base lesion found in DNA. Fortunately, throughout evolution cells have developed repair mechanisms, such as the 8-oxoguanine DNA glycosylases (OGG), which recognize and excise 8-oxoG from DNA thereby preventing the accumulation of deleterious mutations. OGG are divided into three subfamilies, OGG1, OGG2 and AGOG, which are all involved in the base excision repair (BER) pathway. The published structures of OGG1 and AGOG, as well as the recent availability of OGG2 structures in both apo- and liganded forms, provide an excellent opportunity to compare the structural and functional properties of the three OGG subfamilies. Among the observed differences, the three-dimensional fold varies considerably between OGG1 and OGG2 members, as the latter lack the A-domain involved in 8-oxoG binding. In addition, all three OGG subfamilies bind 8-oxoG in a different manner even though the crucial interaction between the enzyme and the protonated N7 of 8-oxoG is conserved. Finally, the three OGG subfamilies differ with respect to DNA binding properties, helix-hairpin-helix motifs, and specificity for the opposite base.
    Full-text · Article · Dec 2012 · International Journal of Molecular Sciences
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    • "In a more recent structure of a catalytically active hOGG1/G@BULLETC–DNA complex that was crosslinked at a more remote location from the lesion (Ser292Cys), the target guanine was fully engaged inside the active site in a virtually identical position as 8oxoG in the LRC. In the IC, however, the guanine remained uncleaved, presumably because it lacks the N7 hydrogen present in 8oxoG that forms a specific hydrogen bond with the carbonyl of Gly42 [72]. The alignment of active site residues other than Gly42 are also important for catalysis, as observed in a phototrapped, uncleaved hOGG1/8oxoG–DNA complex that showed an intact 8oxoG–Gly42 interaction amidst a collection of "
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    ABSTRACT: DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities.
    Full-text · Article · Oct 2012 · Biochimica et Biophysica Acta
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    ABSTRACT: A mechanistic pathway for cleavage of the N-glycosidic bond of 8-oxo-2'-deoxyguanosine (oxoG) catalyzed with the human 8-oxoguanine glycosylase 1 DNA repair protein (hOGG1) is proposed in this theoretical study. The reaction scheme suggests direct proton addition to the glycosidic nitrogen N9 of oxoG from the Nε-ammonium of Lys249 residue of hOGG1 that is enabled owing to the N9 pyramidal geometry. The N9-pyramidalization of oxoG is induced within hOGG1 active site. The coordination of N9 nitrogen to the Nε-ammonium of Lys249 unveiled by available crystal structures enables concerted, synchronous substitution of the N9-C1' bond by the N9-H bond. The reaction is compared with other pathways already proposed by means of calculated activation energies. The ΔG(#) energy for the newly proposed reaction mechanism calculated with the B3LYP/6-31G(d,p) method 17.0 kcal mol(-1) is significantly lower than ΔG(#) energies for other reactions employing attack of the Nε-amino group to the anomeric carbon C1' of oxoG and attack of the Nε-ammonium to the N3 nitrogen of oxoG base. Moreover, activation energy for the oxoG cleavage proceeding via N9-pyramidalization is lower than energy calculated for normal G because the electronic state of the five-membered aromatic ring of oxoG is better suited for the reaction. The modification of aromatic character introduced by oxidation to the nucleobase thus seems to be the factor that is checked by hOGG1 to achieve base-specific cleavage.
    No preview · Article · Sep 2012 · The Journal of Physical Chemistry B
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