Spectroscopic and in vitro Investigations of Fe 2+ /α‐Ketoglutarate‐Dependent Enzymes Involved in Nucleic Acid Repair and Modification

Biomimetic Iron Complex Achieves TET Enzyme Reactivity**

(2021) David Schmidl et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

TET‐Like Oxidation in 5‐Methylcytosine and Derivatives: A Computational and Experimental Study

(2021) Niko S. W. Jonasson et al.   CHEMBIOCHEM

Activity-Based Hydrazine Probes for Protein Profiling of Electrophilic Functionality in Therapeutic Targets

(2021) Zongtao Lin et al.   ACS Central Science

The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism

(2021) Maria Alessandra Martini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Aberrant RNA methylation triggers recruitment of an alkylation repair complex

(2021) Ning Tsao et al.   MOLECULAR CELL

Patient-derived xenografts of different grade gliomas retain the heterogeneous histological and genetic features of human gliomas

(2020) Wenxin Zeng et al.   Cancer Cell International

Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA

(2020) Min Zhang et al.   CELL RESEARCH

Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1

(2020) Li-Fei Tian et al.   CELL RESEARCH

Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster’s Blue in methanol dehydrogenase assays

(2020) Bérénice Jahn et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate–dependent nonheme ferrous enzymes

(2020) Serra Goudarzi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selective targeting of TET catalytic domain promotes somatic cell reprogramming

(2020) Anup Kumar Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation

(2020) L. Y. Kanazhevskaya et al.   RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY

Mitochondrial TCA cycle metabolites control physiology and disease

(2020) Inmaculada Martínez-Reyes et al.   Nature Communications

Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB

(2020) Michael R. Baldwin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reducing agent mediated non‐enzymatic conversion of  2‐oxoglutarate to succinate – implications for oxygenase assays

(2020) Amjad Khan et al.   CHEMBIOCHEM

Active turnover of genomic methylcytosine in pluripotent cells

(2020) Fabio Spada et al.   Nature Chemical Biology

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

(2020) Christopher B. Mulholland et al.   Scientific Reports

Distinct RNAN-demethylation pathways catalyzed by nonheme iron ALKBH5 and FTO enzymes enable regulation of formaldehyde release rates

(2020) Joel D. W. Toh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates

(2019) Xiao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection, Structure and Function of Modified DNA Bases

(2019) Alexandre Hofer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of m6A RNA methylation in cancer

(2019) Ting Sun et al.   BIOMEDICINE & PHARMACOTHERAPY

DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro

(2019) Ke Bian et al.   NUCLEIC ACIDS RESEARCH

Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1

(2019) Shiming Peng et al.   Science Translational Medicine

Membrane Lipidome Reorganization and Accumulation of Tissue DNA Lesions in Tumor-Bearing Mice: An Exploratory Study

(2019) Marios G. Krokidis et al.   Cancers

Regulation Is in the Air: The Relationship between Hypoxia and Epigenetics in Cancer

(2019) Diego Camuzi et al.   Cells

5‐Methylcytosine is Oxidized to the Natural Metabolites of TET Enzymes by a Biomimetic Iron(IV)‐Oxo Complex

(2019) Niko S. W. Jonasson et al.   CHEMISTRY-A EUROPEAN JOURNAL

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

(2019) Christopher W. John et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Additional functions of selected proteins involved in DNA repair

(2019) Vlada Koliadenko et al.   FREE RADICAL BIOLOGY AND MEDICINE

A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB

(2019) Lyubov Yu. Kanazhevskaya et al.   MOLECULES

Real-Time Sensing of TET2-Mediated DNA Demethylation In Vitro by Metal–Organic Framework-Based Oxygen Sensor for Mechanism Analysis and Stem-Cell Behavior Prediction

(2018) Yuzhi Xu et al.   ANALYTICAL CHEMISTRY

O2 Activation by Nonheme FeII α-Ketoglutarate-Dependent Enzyme Variants: Elucidating the Role of the Facial Triad Carboxylate in FIH

(2018) Shyam R. Iyer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of RNA adenosine demethylases in the control of gene expression

(2018) Veronika Rajecka et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides

(2018) Franziska R. Traube et al.   Nature Protocols

Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs

(2018) Zhuojia Chen et al.   NUCLEIC ACIDS RESEARCH

Oxygen gradients can determine epigenetic asymmetry and cellular differentiation via differential regulation of Tet activity in embryonic stem cells

(2017) Simon Burr et al.   NUCLEIC ACIDS RESEARCH

N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing

(2017) Marek Bartosovic et al.   NUCLEIC ACIDS RESEARCH

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding

(2017) Alice R. Walker et al.   PLoS Computational Biology

AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells

(2017) Yuko Ueda et al.   Scientific Reports

Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products

(2016) Long-Fei Wu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

ALKBH1-Mediated tRNA Demethylation Regulates Translation

(2016) Fange Liu et al.   CELL

Role of ALKBH1 in the Core Transcriptional Network of Embryonic Stem Cells

(2016) Rune Ougland et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

NSUN3 and ABH1 modify the wobble position of mt‐tRNAMetto expand codon recognition in mitochondrial translation

(2016) Sara Haag et al.   EMBO JOURNAL

Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage

(2016) Qi Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Spectroscopic analyses of 2-oxoglutarate-dependent oxygenases: TauD as a case study

(2016) Denis A. Proshlyakov et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Tumour hypoxia causes DNA hypermethylation by reducing TET activity

(2016) Bernard Thienpont et al.   NATURE

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

(2016) Peggy Prickaerts et al.   Epigenetics & Chromatin

Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration

(2016) Seung-Gi Jin et al.   Cell Reports

Measurement of Postreplicative DNA Metabolism and Damage in the Rodent Brain

(2015) Jay P. Patel et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Oncometabolites: tailoring our genes

(2015) Stefan Nowicki et al.   FEBS Journal

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond

(2015) Bogdan I. Fedeles et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fumarate and Succinate Regulate Expression of Hypoxia-inducible Genes via TET Enzymes

(2015) Tuomas Laukka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fluorescein Derivatives as Bifunctional Molecules for the Simultaneous Inhibiting and Labeling of FTO Protein

(2015) Tianlu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural insight into substrate preference for TET-mediated oxidation

(2015) Lulu Hu et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Structure ofNaegleriaTet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

(2015) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

The broad spectrum 2-oxoglutarate oxygenase inhibitor N-oxalylglycine is present in rhubarb and spinach leaves

(2015) Khalid Al-Qahtani et al.   PHYTOCHEMISTRY

A strategy based on nucleotide specificity leads to a subfamily-selective and cell-active inhibitor of N6-methyladenosine demethylase FTO

(2015) Joel D. W. Toh et al.   Chemical Science

Non-homologous functions of the AlkB homologs

(2015) Rune Ougland et al.   Journal of Molecular Cell Biology

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues

(2014) Chenxu Zhu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Pyrene-Based Quantitative Detection of the 5-Formylcytosine Loci Symmetry in the CpG Duplex Content during TET-Dependent Demethylation

(2014) Liang Xu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Rate-Limiting Step of O2 Activation in the α-Ketoglutarate Oxygenase Factor Inhibiting Hypoxia Inducible Factor

(2014) John A. Hangasky et al.   BIOCHEMISTRY

TET-catalyzed 5-methylcytosine hydroxylation is dynamically regulated by metabolites

(2014) Hui Yang et al.   CELL RESEARCH

Mechanism of Repair of Acrolein- and Malondialdehyde-Derived Exocyclic Guanine Adducts by the α-Ketoglutarate/Fe(II) Dioxygenase AlkB

(2014) Vipender Singh et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Crystal structure of the RNA demethylase ALKBH5 from zebrafish

(2014) Weizhong Chen et al.   FEBS LETTERS

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

(2014) Sabrina Harteis et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Atomic Resolution Structure of Human AlkB Homolog 7 (ALKBH7), a Key Protein for Programmed Necrosis and Fat Metabolism

(2014) Guoqiang Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of theEscherichia coliDNA-Repair Enzyme AlkB

(2014) Burçe Ergel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structures of the Human RNA Demethylase Alkbh5 Reveal Basis for Substrate Recognition

(2014) Chong Feng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation

(2014) WeiShen Aik et al.   NUCLEIC ACIDS RESEARCH

Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5

(2014) Yue Huang et al.   NUCLEIC ACIDS RESEARCH

Geometric and Electronic Structure Contributions to Function in Non-heme Iron Enzymes

(2013) Edward I. Solomon et al.   ACCOUNTS OF CHEMICAL RESEARCH

A covalent protein–DNA 5′-product adduct is generated following AP lyase activity of human ALKBH1 (AlkB homologue 1)

(2013) Tina A. Müller et al.   BIOCHEMICAL JOURNAL

Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation

(2013) Lulu Hu et al.   CELL

Removal of N-Alkyl Modifications from N2-Alkylguanine and N4-Alkylcytosine in DNA by the Adaptive Response Protein AlkB

(2013) Deyu Li et al.   CHEMICAL RESEARCH IN TOXICOLOGY

NMR methods for structural studies of large monomeric and multimeric proteins

(2013) Dominique P Frueh et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Oncometabolites: linking altered metabolism with cancer

(2013) Ming Yang et al.   JOURNAL OF CLINICAL INVESTIGATION

Structural Basis for Inhibition of the Fat Mass and Obesity Associated Protein (FTO)

(2013) WeiShen Aik et al.   JOURNAL OF MEDICINAL CHEMISTRY

Elucidation of the Fe(iv)=O intermediate in the catalytic cycle of the halogenase SyrB2

(2013) Shaun D. Wong et al.   NATURE

Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA

(2013) Hideharu Hashimoto et al.   NATURE

CGmCGCG is a versatile substrate with which to evaluate Tet protein activity

(2013) Seiichiro Kizaki et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation

(2013) Richard J. Hopkinson et al.   Chemical Science

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Changes in Protein Dynamics of the DNA Repair Dioxygenase AlkB upon Binding of Fe2+ and 2-Oxoglutarate

(2012) Boris Bleijlevens et al.   BIOCHEMISTRY

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development

(2012) Yufei Xu et al.   CELL

The Schizosaccharomyces pombe AlkB homolog Abh1 exhibits AP lyase activity but no demethylase activity

(2012) Hanne Korvald et al.   DNA REPAIR

AlkB Dioxygenase Preferentially Repairs Protonated Substrates

(2012) Agnieszka M. Maciejewska et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Surface Plasmon Resonance Spectroscopy: A Versatile Technique in a Biochemist’s Toolbox

(2012) Ray Bakhtiar   JOURNAL OF CHEMICAL EDUCATION

Dynamic Combinatorial Mass Spectrometry Leads to Inhibitors of a 2-Oxoglutarate-Dependent Nucleic Acid Demethylase

(2012) Esther C. Y. Woon et al.   JOURNAL OF MEDICINAL CHEMISTRY

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Duplex interrogation by a direct DNA repair protein in search of base damage

(2012) Chengqi Yi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ALKBH1 is a Histone H2A Dioxygenase Involved in Neural Differentiation

(2012) Rune Ougland et al.   STEM CELLS

Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4

(2011) Linn G. Bjørnstad et al.   BIOCHEMICAL JOURNAL

Evidence for the Mechanism of Hydroxylation by 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase from Intermediate Partitioning in Active Site Variants

(2011) Dhara D. Shah et al.   BIOCHEMISTRY

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

(2011) Wei Xu et al.   CANCER CELL

Crystal Structure and RNA Binding Properties of the RNA Recognition Motif (RRM) and AlkB Domains in Human AlkB Homolog 8 (ABH8), an Enzyme Catalyzing tRNA Hypermodification

(2011) Chiara Pastore et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA Unwinding by ASCC3 Helicase Is Coupled to ALKBH3-Dependent DNA Alkylation Repair and Cancer Cell Proliferation

(2011) Sebastian Dango et al.   MOLECULAR CELL

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Human AlkB Homologue 5 Is a Nuclear 2-Oxoglutarate Dependent Oxygenase and a Direct Target of Hypoxia-Inducible Factor 1α (HIF-1α)

(2011) Armin Thalhammer et al.   PLoS One

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

(2011) Erwin van den Born et al.   Nature Communications

Graphene chiral liquid crystals and macroscopic assembled fibres

(2011) Zhen Xu et al.   Nature Communications

Fluorescence anisotropy: from single molecules to live cells

(2010) Claudiu C. Gradinaru et al.   ANALYST

The AlkB Domain of Mammalian ABH8 Catalyzes Hydroxylation of 5-Methoxycarbonylmethyluridine at the Wobble Position of tRNA

(2010) Ye Fu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Monitoring the Activity of 2-Oxoglutarate Dependent Histone Demethylases by NMR Spectroscopy: Direct Observation of Formaldehyde

(2010) Richard J. Hopkinson et al.   CHEMBIOCHEM

Evidence for the slow reaction of hypoxia-inducible factor prolyl hydroxylase 2 with oxygen

(2010) Emily Flashman et al.   FEBS Journal

Mutual Relationship between Stacking and Hydrogen Bonding in DNA. Theoretical Study of Guanine−Cytosine, Guanine−5-methylcytosine, and Their Dimers

(2010) Carles Acosta-Silva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mammalian ALKBH8 Possesses tRNA Methyltransferase Activity Required for the Biogenesis of Multiple Wobble Uridine Modifications Implicated in Translational Decoding

(2010) L. Songe-Moller et al.   MOLECULAR AND CELLULAR BIOLOGY

Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase

(2010) Chengqi Yi et al.   NATURE

Crystal structure of the FTO protein reveals basis for its substrate specificity

(2010) Zhifu Han et al.   NATURE

Divergent β-hairpins determine double-strand versus single-strand substrate recognition of human AlkB-homologues 2 and 3

(2010) Vivi Talstad Monsen et al.   NUCLEIC ACIDS RESEARCH

Structure determination of DNA methylation lesions N 1 -meA and N 3 -meC in duplex DNA using a cross-linked protein–DNA system

(2010) Lianghua Lu et al.   NUCLEIC ACIDS RESEARCH

Structural and Mutational Analysis of Escherichia coli AlkB Provides Insight into Substrate Specificity and DNA Damage Searching

(2010) Paul J. Holland et al.   PLoS One

Insight into the mechanism of an iron dioxygenase by resolution of steps following the FeIVboxHO species

(2010) P. K. Grzyska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human AlkB homologue 1 (ABH1) exhibits DNA lyase activity at abasic sites

(2009) Tina A. Müller et al.   DNA REPAIR

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

(2009) Lenny Dang et al.   NATURE

Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB

(2009) B. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

Dynamic states of the DNA repair enzyme AlkB regulate product release

(2008) Boris Bleijlevens et al.   EMBO REPORTS

Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO

(2008) Guifang Jia et al.   FEBS LETTERS

Human AlkB Homolog 1 Is a Mitochondrial Protein That Demethylates 3-Methylcytosine in DNA and RNA

(2008) Marianne Pedersen Westbye et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA

(2008) Cai-Guang Yang et al.   NATURE

Viral AlkB proteins repair RNA damage by oxidative demethylation

(2008) Erwin van den Born et al.   NUCLEIC ACIDS RESEARCH

Isothermal titration calorimetry of metal ions binding to proteins: An overview of recent studies

(2007) Dean E. Wilcox   INORGANICA CHIMICA ACTA