Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage

Sundheim, Ottar; Vågbø, Cathrine Broberg; Bjørås, Magnar; Sousa, Mirta Mittelstedt Leal de; Talstad, Vivi; Arne, Per; Drabløs, Finn; Krokan, Hans E.; Tainer, John A.; Slupphaug, Geir

doi:10.1038/sj.emboj.7601219

Cited by 166 publications

(234 citation statements)

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“…The authors suggest that ABH3 binds its DNA substrate in a direction opposite to that in AlkB. 79 In contrast to the primary substrate, αKG is bound similarly in these dioxygenases. The crystal structure also reveals several new key residues important for ABH3 activity.…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

“…6). 79 The structure contains the typical core of Fe II /αKG-dependent dioxygenases, and includes the iron-binding ligands His 191, Asp 193 and His 257 as well as Arg 269 which forms a salt bridge with αKG. A hairpin formed by β4 and β5 creates a lid over the active site and a positively charged groove constitutes the DNA and RNA binding cleft.…”

Section: Mammalian Alkb Homologuesmentioning

confidence: 99%

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FeII/α-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism

2008

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Fe II /α-ketoglutarate-dependent hydroxylases uniformly possess a double-stranded β-helix fold with two conserved histidines and one carboxylate coordinating their mononuclear ferrous ions. Oxidative decomposition of the α-keto acid is proposed to generate a ferryl-oxo intermediate capable of hydroxylating unactivated carbon atoms in a myriad of substrates. This perspective focuses on a subgroup of these enzymes that are involved in pyrimidine salvage, purine decomposition, nucleoside and nucleotide hydroxylation, DNA/RNA repair, and chromatin modification. The varied reaction schemes are presented, and selected structural and kinetic information is summarized. IntroductionFerrous ion and α-ketoglutarate (αKG)-dependent dioxygenases comprise an enzyme superfamily with members present in animals, plants, protists, fungi, bacteria and even viruses. Most representatives of this large group of enzymes couple the oxidative decarboxylation of αKG to various hydroxylation reactions ( Fig. 1), but others are capable of catalyzing desaturation, epoxidation, halogenation, ring formation, or ring expansion reactions, which allows them to fill a wide variety of biological roles including antibiotic biosynthesis, hypoxic sensing, DNA repair, and various types of metabolite transformations. [1][2][3] Not surprisingly, the primary substrates also are diverse and include proteins, lipids, nucleic acids, and a myriad of small molecules that can be used for synthesis or undergo degradation.The sequences of Fe II /αKG dioxygenases show little overall identity, yet the diverse reactions all are catalyzed by proteins with the same core fold and use similar chemistries. 4 The hallmark of these enzymes is their use of Fe II to activate molecular oxygen according to a mechanism (Scheme 1) first proposed by Hanauske-Abel and Günzler in 1982 for prolyl 4-hydroxylase. 5 (A) In the absence of substrates, a "facial triad" (usually two His plus one Asp or Glu occurring in a His-X-Asp/Glu-X n -His motif) weakly bind one face of the hexacoordinate metal. 6,7 (B) The αKG co-substrate displaces two waters and coordinates Fe II in a bidentate fashion with its C1 carboxyl and C2 keto oxygens. The binding of αKG is Correspondence to: Robert P. Hausinger, hausinge@msu.edu. NIH Public Access Author ManuscriptDalton Trans. Author manuscript; available in PMC 2010 July 20. This perspective focuses on the modification of nucleobases, nucleosides, nucleotides, and chromatin by the Fe II and αKG dependent hydroxylases (Table 1). We discuss the degradation and salvage of free bases by the fungal enzymes thymine 7-hydroxylase and xanthine hydroxylase. Next, nucleoside hydroxylases are briefly described. We then examine the developmental modification of DNA in kinetoplastid protozoans and summarize evidence that the JBP1 and JBP2 proteins possess thymidine hydroxylase activity. The oxidative repair of DNA by Escherichia coli AlkB is discussed, and the properties of mammalian homologues are summarized. Finally, we present emerging evidence pointing to...

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Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

Section: Mammalian Alkb Homologuesmentioning

confidence: 99%

FeII/α-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism

2008

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“…The housekeeping enzyme in mammalian cells, ALKBH2, plays a crucial role in pediatric brain tumors during chemotherapy treatment (20). Essential for prostate cancer progression, ALKBH3 presents a potential target for effective therapy in prostate cancer (21,22).Structural characterizations of AlkB repair enzymes have provided insights into the understanding of demethylation mechanism and substrate recognition (23)(24)(25)(26). Similar to members of the 2OG-dioxygenase family, 2OG could inhibit AlkB at high concentrations (27).…”

mentioning

confidence: 99%

“…Structural characterizations of AlkB repair enzymes have provided insights into the understanding of demethylation mechanism and substrate recognition (23)(24)(25)(26). Similar to members of the 2OG-dioxygenase family, 2OG could inhibit AlkB at high concentrations (27).…”

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confidence: 99%

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

Huang

Liu

et al. 2016

Journal of Biological Chemistry

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The AlkB repair enzymes, including Escherichia coli AlkB and two human homologues, ALKBH2 and ALKBH3, are iron(II)-and 2-oxoglutarate-dependent dioxygenases that efficiently repair N 1 -methyladenine and N 3 -methylcytosine methylated DNA damages. The development of small molecule inhibitors of these enzymes has seen less success. Here we have characterized a previously discovered natural product rhein and tested its ability to inhibit AlkB repair enzymes in vitro and to sensitize cells to methyl methane sulfonate that mainly produces N 1 -methyladenine and N 3 -methylcytosine lesions. Our investigation of the mechanism of rhein inhibition reveals that rhein binds to AlkB repair enzymes in vitro and promotes thermal stability in vivo. In addition, we have determined a new structural complex of rhein bound to AlkB, which shows that rhein binds to a different part of the active site in AlkB than it binds to in fat mass and obesity-associated protein (FTO). With the support of these observations, we put forth the hypothesis that AlkB repair enzymes would be effective pharmacological targets for cancer treatment.The nucleic acids in living cells are subject to modification by both endogenous and environmental agents (1). Direct-acting chemicals constantly damage nucleic acids and generate various methyl lesions with mutagenic and/or cytotoxic consequences (2, 3). O 6 -Methylguanine (O 6 mG) 2 and N 3 -methyladenine lesions have the highest potential for methylating damage by an SN1 agent such as N-methyl-NЈ-nitro-N-nitrosoguanidine (MNNG), which block replication and are thought to be toxic (4, 5). For the most part, the SN2 agent such as methyl methane sulfonate (MMS) produces N 1 -methyladenine (m 1 A) and N 3 -methylcytosine (m 3 C) lesions in single-stranded DNA (ssDNA). Accumulation of these adducts can lead to cell death (6, 7). Organisms have evolved several mechanisms to efficiently remove various methyl lesions, including suicidal methyltransferases, DNA glycosylases, and the AlkB family dioxygenases (see Fig. 1A) (8, 9). To date, AlkB repair appears to be the major natural defense mechanism with the power to restore the canonical base structure in vivo. Escherichia coli AlkB and its human homologues, ALKBH2 and ALKBH3, utilize iron(II) and 2-oxoglutarate (2OG) to achieve oxidative demethylation of m 1 A and m 3 C (see Fig. 1B) (10 -12). The lack of AlkB repair results in increased sensitivity to MMS, elevated level of mutations, and reduced cell proliferation (13-16). Furthermore, the accumulation of m 1 A and m 3 C lesions could also occur on RNA. Research suggests that the oxidative demethylation in mRNA and tRNA acts as a part of AlkB or ALKBH3 repair to protect cells against MMS (17, 18). The scope of substrates for AlkB repair has been largely extended to all simple N-alkyl lesions at the WatsonCrick base-pairing interface on the four bases (19), thus indicating the importance of oxidative demethylation for cell survival. In addition, human enzymes have been broadly linked to cancer. The housekeeping ...

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“…So far, several crystal structures of AlkB members, including AlkB, hABH2 and hABH3, have been solved (Sundheim et al, 2006;Yu et al, 2006;Yang et al, 2008). As expected, all the available structures reveal a conserved double-stranded beta-helix (DSBH) fold, termed as jelly-roll motif that coordinates a catalytically active iron center composed of a conserved His-Xaa-Asp/Glu-Xaa-His motif (Hausinger, 2004).…”

Section: Alkb-family Dna/rna Demethylase and Substrate Selection Mechmentioning

confidence: 65%

A loop matters for FTO substrate selection

et al. 2010

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Recent studies have unequivocally established the link between FTO and obesity. FTO was biochemically shown to belong to the AlkB-like family DNA/RNA demethylase. However, FTO differs from other AlkB members in that it has unique substrate specificity and contains an extended C-terminus with unknown functions. Insight into the substrate selection mechanism and a functional clue to the C-terminus of FTO were gained from recent structural and biochemical studies. These data would be valuable to design FTO-specific inhibitors that can be potentially translated into therapeutic agents for treatment of obesity or obesity-related diseases.

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Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage

Cited by 166 publications

References 51 publications

FeII/α-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism

FeII/α-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism

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

A loop matters for FTO substrate selection

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