An Iron-Sulfur Cluster in the Family 4 Uracil-DNA Glycosylases

Hinks, John A.; Evans, M.C.W.; Miguel, Yolanda R. de; Sartori, Alessandro A.; Jiricny, Josef; Pearl, Laurence H.

doi:10.1074/jbc.m200668200

Cited by 70 publications

(75 citation statements)

References 28 publications

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“…It is interesting to note that other organisms also contain BER repair proteins with an ironsulfur cofactor [9,10]. Most notably, in a set of thermophilic organisms, there is a uracil DNA glycosylase (UDG) that contains a [4Fe-4S] cluster [9].…”

Section: A Model For Damage Detection Through Dna Charge Transportmentioning

confidence: 99%

“…Most notably, in a set of thermophilic organisms, there is a uracil DNA glycosylase (UDG) that contains a [4Fe-4S] cluster [9]. This is especially noteworthy given that the primary process that leads to uracil in DNA, cytosine deamination, has an enhanced rate at high temperatures [61].…”

Section: A Model For Damage Detection Through Dna Charge Transportmentioning

confidence: 99%

“…Many BER glycosylases contain a [4Fe-4S] cluster [8][9][10], the function of which is unknown. Endonuclease III (Endo III) was the first glycosylase discovered to contain this metal cofactor [8].…”

Section: Introductionmentioning

confidence: 99%

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DNA repair glycosylases with a [4Fe–4S] cluster: A redox cofactor for DNA-mediated charge transport?

Boal

Yavin

Barton

2007

Journal of Inorganic Biochemistry

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The [4Fe-4S] cluster is ubiquitous to a class of base excision repair enzymes, in organisms ranging from bacteria to man, and was first considered as a structural element, owing to its redox stability under physiological conditions. When studied bound to DNA, two of these repair proteins (MutY and Endonuclease III from Escherichia coli) display DNA-dependent reversible electron transfer with characteristics typical of high potential iron proteins. These results have inspired a reexamination of the role of the [4Fe-4S] cluster in this class of enzymes. Might the [4Fe-4S] cluster be used as a redox cofactor to search for damaged sites using DNA-mediated charge transport, a process well known to be highly sensitive to lesions and mismatched bases? Described here are experiments demonstrating the utility of DNA-mediated charge transport in characterizing these DNA-binding metalloproteins, as well as efforts to elucidate this new function for DNA as an electronic signaling medium among the proteins.

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Section: A Model For Damage Detection Through Dna Charge Transportmentioning

confidence: 99%

Section: A Model For Damage Detection Through Dna Charge Transportmentioning

confidence: 99%

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DNA repair glycosylases with a [4Fe–4S] cluster: A redox cofactor for DNA-mediated charge transport?

Boal

Yavin

Barton

2007

Journal of Inorganic Biochemistry

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“…Overall, this process provides a rationale for the widespread distribution of redox cofactors in DNA repair proteins (1)(2)(3)(4)(5)(6)(7)(31)(32)(33)(34)(35)(36)(37). Through this route, the rapid scanning of the genome can be accomplished by using few copies of repair protein.…”

Section: Redox Properties Of Muty and Hipip Iron Proteinsmentioning

confidence: 99%

DNA-mediated charge transport for DNA repair

Boon

Livingston

Chmiel

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

223

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MutY, like many DNA base excision repair enzymes, contains a [4Fe4S] 2؉ cluster of undetermined function. Electrochemical studies of MutY bound to a DNA-modified gold electrode demonstrate that the [4Fe4S] cluster of MutY can be accessed in a DNA-mediated redox reaction. Although not detectable without DNA, the redox potential of DNA-bound MutY is Ϸ275 mV versus NHE, which is characteristic of HiPiP iron proteins. Binding to DNA is thus associated with a change in [4Fe4S] 3؉/2؉ potential, activating the cluster toward oxidation. Given that DNA charge transport chemistry is exquisitely sensitive to perturbations in base pair structure, such as mismatches, we propose that this redox process of MutY bound to DNA exploits DNA charge transport and provides a DNA signaling mechanism to scan for mismatches and lesions in vivo.D NA repair proteins that contain a FeS redox cofactor are ubiquitous (1-7), yet a role for these factors has been lacking. Two examples, highly homologous (8), are MutY (1) and endonuclease III (Endo III) (2, 9), base excision repair enzymes from Escherichia coli (10). MutY, containing 350 residues, acts as a glycosylase to remove adenine from G:A (11-13) and 7,8-dihydro-8-oxo-2-deoxyguanonsine:A mismatches (14-21); Endo III removes pyrimidines damaged by ring saturation, contraction, or fragmentation (22-29). Although MutY and Endo III have dramatically different substrate recognition features, they both contain a [4Fe4S] 2ϩ cluster (1, 2, 9) within a Cys-X 6 -Cys-X 2 -Cys-X 5 -Cys loop located near the protein C terminus (1, 9, 30). Based on sequence alignment, a loop defined by the first two ligating cysteines, called the FCL, is proposed to be a common element of DNA repair proteins (30), present throughout phylogeny (31-37). The function, if any, for these clusters remains undetermined, although the FCL has been proposed as a structural element, aiding in DNA binding (9,30,38). Interestingly, however, MutY is capable of folding without the cluster; the [4Fe4S] 2ϩ cluster adds no stability to the enzyme, but it is critical for substrate binding and catalysis (39). The solvent-accessible [4Fe4S] 2ϩ cluster of Endo III undergoes decomposition with ferricyanide and is resistant to reduction, with an estimated midpoint potential of ϽϪ600 mV for the [4Fe4S] 2ϩ/1ϩ couple (2, 38).Here, we consider whether the [4Fe4S] 2ϩ cluster in MutY can function in DNA-mediated charge transport (CT). Many laboratories have probed DNA-mediated CT chemistry (40-42). Using biochemical, spectroscopic, and electrochemical methods, we have shown that CT through DNA can proceed over long molecular distances in a reaction that is remarkably sensitive to intervening dynamical base pair structure (43-50). DNAmediated CT has been shown to yield oxidative DNA damage from a distance within nucleosome core particles (47) and HeLa cell nuclei (51). DNA binding proteins and peptides have also been shown to modulate and participate in long-range CT chemistry (48, 49), raising the question of the physiological relevance of DNA CT....

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“…The 2ϩ HiPiPs are readily oxidized by ferricyanide (24). The FeS cluster in family 4 uracil-DNA glycosylases was recently shown to have redox properties of HiPiPs (25).…”

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confidence: 99%

Redox Reactions of the Iron-Sulfur Cluster in a Ribosomal RNA Methyltransferase, RumA

Agarwalla

Stroud

Gaffney

2004

Journal of Biological Chemistry

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RumA, an S-adenosyl-L-methionine-dependent methyltransferase specifically catalyzes the methylation of U1939 of 23 S ribosomal RNA to yield 5-methyluridine (m 5 U) 1 or ribothymidine (1). This enzyme was found to contain a [4Fe-4S] cluster, a prosthetic group usually not associated with methyltransferase enzymes. The x-ray structure of RumA revealed that the cluster is located in the RNA binding domain of the threedomain protein (2). It is held by four Cys-iron bonds provided by Cys 81 , Cys 87 , Cys 90 , and Cys 162 and is buried in a largely hydrophobic region, but one of its sulfur atoms is quite exposed to solvent. The closest distance between the cluster and the sulfur of the catalytic nucleophile, Cys 389 , is ϳ19 Å. RumA is a member of a growing list of nucleic acid modifying enzymes where the function of the iron-sulfur (FeS) cluster remains enigmatic.The reaction mechanism of m 5 U methyltransferases is similar to that of thymidylate synthase, and has been studied mainly employing the tRNA m 5 U54 methyltransferase, TrmA (3-5). It involves Michael addition of the catalytic Cys to carbon 6 (C-6) of pyrimidine, which activates C-5 for a nucleophilic attack on the methyl group of S-adenosyl-L-methionine. Following the methyl transfer, the enzyme is resolved by abstraction of a proton from C-5 and ␤-elimination. TrmA, as well as DNA and RNA 5-methylcytidine methyltransferases, which employ a similar catalytic mechanism (6), do not posses an FeS cluster or any other prosthetic group. Lack of a redox step in the catalytic mechanism, and absence of the cluster in enzymes that employ a similar mechanism preclude a direct role for [4Fe-4S] cluster in the RumA-catalyzed reaction.Two features distinguish the FeS cluster in RumA from the clusters in a different class of S-adenosyl-L-methionine-dependent enzymes that proceed by free radical mechanisms. The RumA cluster is ligated by 4 cysteines and the iron-binding sequence motif is CX 5 CX 2 CX n C. In contrast, the radical Sadenosyl-L-methionine enzymes, of which MiaB (7) and biotin synthase (8) are examples, have a [4Fe-4S] cluster built of a CX 3 CX 2 C sequence that leaves one iron of the cluster free to participate in catalysis. MiaB is a member of a family of enzymes catalyzing addition of sulfur to tRNA bases (9). The FeS sequence motifs in the DNA repair enzymes, endonuclease III (10) and MutY (11), are CX 6 CX 2 CX 5 C, somewhat similar to the RumA sequence. Although the FeS clusters in these enzymes are usually regarded as structural, recently it was shown that the redox potential of MutY is altered by DNA binding and that a change in charge of the [4Fe-4S] 3ϩ/2ϩ cluster might alter its affinity for DNA (12).The redox potentials of [4Fe-4S] clusters vary widely (13-16). Of particular interest in many contemporary studies of FeS proteins is understanding the factors that influence the potentials, and thus functions, of these clusters (17,18). Proteins with four Cys-iron bonds to the [4Fe-4S] cluster fall into two general redox groups, ones with an accessib...

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An Iron-Sulfur Cluster in the Family 4 Uracil-DNA Glycosylases

Cited by 70 publications

References 28 publications

DNA repair glycosylases with a [4Fe–4S] cluster: A redox cofactor for DNA-mediated charge transport?

DNA repair glycosylases with a [4Fe–4S] cluster: A redox cofactor for DNA-mediated charge transport?

DNA-mediated charge transport for DNA repair

Redox Reactions of the Iron-Sulfur Cluster in a Ribosomal RNA Methyltransferase, RumA

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