ArticleChemistry (Weinheim an der Bergstrasse, Germany)2014
Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes.
Article in Chemistry (Weinheim an der Bergstrasse, Germany), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 140 citations in OpenAlex.
- Beyond Histone Demethylation: Mechanisms ofJACS Au · 2026Article
- Mechanistic insights into the selective oxidation of D-arginine by the nonheme iron-dependent viomycin biosynthesis enzyme VioC.iScience · 2025Article
- Revealing the catalytic mechanism of the Fe(II)/2-oxoglutarate-dependent human epigenetic modifying enzyme ALKBH5.Cell reports. Physical science · 2025Article
- Catalytic Mechanism of the Bacterial Non-Heme Fe(II) and 2-Oxoglutarate Dependent Enzyme AlkB with Single-Stranded DNA Containing Complex Guanine Adducts.Inorganic chemistry · 2025Article
- C-C Bond Cleavage in the Late-Stage Biosynthesis of Huperzine Alkaloids Occurs via Enzymatic Retro-Aza-Prins Reaction.Journal of the American Chemical Society · 2025Article
- Origins of Catalysis in Non-Heme Fe(II)/2-Oxoglutarate-Dependent Histone Lysine Demethylase KDM4A with Differently Methylated Histone H3 Peptides.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Article
- Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH.Chemphyschem : a European journal of chemical physics and physical chemistry · 2024Article
- The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A.Inorganic chemistry · 2024Article
- Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH.Chemical science · 2024Article
- Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes.Frontiers in chemistry · 2024Review
- Revealing the Catalytic Strategy of FTO.Chem catalysis · 2023Article
- Catalysis by KDM6 Histone Demethylases - A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Article
- Quantum based effects of therapeutic nuclear magnetic resonance persistently reduce glycolysis.iScience · 2022Article
- How Human TET2 Enzyme Catalyzes the Oxidation of Unnatural Cytosine Modifications in Double-Stranded DNA.ACS catalysis · 2022Article
- Electrostatic Perturbations in the Substrate-Binding Pocket of Taurine/α-Ketoglutarate Dioxygenase Determine its Selectivity.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families.Physical chemistry chemical physics : PCCP · 2021Review
- What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations.RSC advances · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
Abstract
AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N(1) -methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)-oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ- and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.