Guanine bases in DNA G-quadruplex adopt nonplanar geometries owing to solvation and base pairing

Mechanism of Rate Acceleration of Radical C-C Bond Formation Reaction by a Radical SAM GTP 3',8-Cyclase

While the number of characterized radical S-adenosyl-l-methionine (SAM) enzymes is increasing, the roles of these enzymes in radical catalysis remain largely ambiguous. In radical SAM enzymes, the slow radical initiation step kinetically masks the subsequent steps, making it impossible to study the kinetics of radical chemistry. Due to this kinetic masking, it is unknown whether the subsequent radical reactions require rate acceleration by the enzyme active site. Here, we report the first evidence that a radical SAM enzyme MoaA accelerates the radical-mediated C-C bond formation. MoaA catalyzes an unprecedented 3',8-cyclization of GTP into 3',8-cyclo-7,8-dihydro-GTP (3',8-cH₂GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterizations, we found that MoaA catalyzes a shunt pathway in which an on-pathway intermediate, GTP C-3' radical, abstracts H-4' atom from (4'R)-5'-deoxyadenosine (5'-dA) to transiently generate 5'-deoxyadenos-4'-yl radical (5'-dA-C4'^•) that is subsequently reduced stereospecifically to yield (4'S)-5'-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics and determined the rate of the on-pathway 3',8-cyclization step as 2.7 ± 0.7 s^-1. Together with DFT calculations, this observation suggested that the 3',8-cyclization by MoaA is accelerated by 6-9 orders of magnitude. Further experimental and theoretical characterizations suggested that the rate acceleration is achieved mainly by constraining the triphosphate and guanine base positions while leaving the ribose flexible, and a transition state stabilization through H-bond and electrostatic interactions with the positively charged R17 residue. This is the first evidence for rate acceleration of radical reactions by a radical SAM enzyme and provides insights into the mechanism by which radical SAM enzymes accelerate radical chemistry.

The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine

The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme–substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG^# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG^# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH₃⁺(Lys249) and CO₂⁻(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with ¹H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.

The activation of N-glycosidic bond cleavage performed by base-excision repair enzyme hOGG1; theoretical study of the role of Lys 249 residue in activation of G, OxoG and FapyG

NLMOs of lone-pair electrons at N9 nitrogen and Fukui indexesf²of N9.

Pyramidalization of the glycosidic nitrogen provides the way for efficient cleavage of the N-glycosidic bond of 8-OxoG with the hOGG1 DNA repair protein

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.