Catalytic Mechanism of Nogalamycin Monoxygenase: How Does Nature Synthesize Antibiotics without a Metal Cofactor?

Abstract

Nogalamycin monoxygenase (NMO) is a member of a family of enzymes that catalyze a key step in the biosynthesis of tetracycline antibiotics, used to treat, e.g., breast cancer in humans, using molecular oxygen for substrate oxidation but without an apparent cofactor. As most monoxygenases and dioxygenases contain a transition metal center (Fe/Cu) or flavin, this begs the question how NMO catalyzes this unusual oxygen atom transfer reaction from molecular oxygen to substrate directly. We performed a detailed computational study on the mechanism and catalytic cycle of NMO using density functional theory and quantum mechanics/molecular mechanics (QM/MM) on the full protein. We considered the substrate in various protonation states and its reaction with oxidant O 2 as well as O 2- through either electron transfer, proton transfer or hydrogen atom transfer. The lowest energy pathway for the models presented here is a reaction of the neutral substrate with a superoxo anion radical (O 2-). In the absence of available free superoxo anions, however,

DpgC‐Catalyzed Peroxidation of 3,5‐Dihydroxyphenylacetyl‐CoA (DPA‐CoA): Insights into the Spin‐Forbidden Transition and Charge Transfer Mechanisms**

“…The presence of the protein environment stabilizes the charge on the O , shifting this energy to 36.6 kcal mol −1 . This value, however, is significantly larger than that calculated for the reaction between O 2 and flavin, 2.8 kcal mol −1 at a DFT level (and implicit water solvent) [30] . This difference may explain why enzymes use flavin as a redox catalyzer.…”

“…Indeed, the position of the two water molecules that are close to O 2 and C α is very similar in the crystal. Regarding these water molecules, it could have been expected that one of the water molecules could protonate the triplet O 2 as was predicted for the reaction between O 2 and flavin [28, 30, 33] . However, at the MECP, the proton is still on the water.…”

“…This means that proton transfer occurs significantly after the peroxide is formed. Probably, that is the reason why there are not basic residues around the active site that could donate a proton to O 2 , as was observed for other cofactorless reactions [28, 30, 33] . Proton transfer drifts the system away from the MECP and, even in the minimum associated with the singlet state, the proton is only shared between the peroxide and the water.…”

“…For typical values of SOC, the hopping probability lies between 0.001 and 0.1, which is equivalent to an increase in the activation energy of 1–4 kcal mol −1 at room temperature [47, 49] . Similar methodologies have been successfully applied to the study of some enzymatic reactions, [15, 28–33, 44, 52, 53] including glucose oxidase [32, 33] and p ‐hydroxyphenylacetate hydroxylase, [28] for which O 2 reacts with flavin, as well as the cofactorless oxygenases (1 H )‐3‐hydroxy‐4‐oxoquinaldine 2,4‐dioxygenase (HOD) [29, 31] and nogalamycin monoxygenase, [30] some of them using small active site models.…”

SILVER SULFATE (Ag2SO4): MOLECULAR ANALYSIS AND ION TRANSPORT

“…Maka dari itu, pasangan 2. Analisis keberadaan pasangan elektron bebas (125)(126)(127)(128)(129)(130)(131)(132)(133)(134)(135) dengan cara pilih bagian structure, pilih lone pair kemudian pilih add, maka akan tampil pasangan elektron bebas (125)(126)(127)(128)(129)(130)(131)(132)(133)(134)(135) dari masing-maisng molekul. 3.…”