The Experts below are selected from a list of 249 Experts worldwide ranked by ideXlab platform
James T Stivers - One of the best experts on this subject based on the ideXlab platform.
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solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3 Methyladenine dna glycosylase i
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, Alexander C Drohat, Yu Lin Jiang, James T StiversAbstract:Abstract The specific recognition mechanisms of DNA repair glycosylases that remove cationic alkylpurine bases in DNA are not well understood partly due to the absence of structures of these enzymes with their cognate bases. Here we report the solution structure of 3-Methyladenine DNA glycosylase I (TAG) in complex with its 3-Methyladenine (3-MeA) cognate base, and we have used chemical perturbation of the base in combination with mutagenesis of the enzyme to evaluate the role of hydrogen bonding and π-cation interactions in alkylated base recognition by this DNA repair enzyme. We find that TAG uses hydrogen bonding with heteroatoms on the base, van der Waals interactions with the 3-Me group, and conventional π-π stacking with a conserved Trp side chain to selectively bind neutral 3-MeA over the cationic form of the base. Discrimination against binding of the normal base adenine is derived from direct sensing of the 3-methyl group, leading to an induced-fit conformational change that engulfs the base in a box defined by five aromatic side chains. These findings indicate that base specific recognition by TAG does not involve strong π-cation interactions, and suggest a novel mechanism for alkylated base recognition and removal.
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a novel zinc snap motif conveys structural stability to 3 Methyladenine dna glycosylase i
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, James T StiversAbstract:Abstract The Escherichia coli 3-Methyladenine DNA glycosylase I (TAG) is a DNA repair enzyme that excises 3-Methyladenine in DNA and is the smallest member of the helix-hairpin-helix (HhH) superfamily of DNA glycosylases. Despite many studies over the last 25 years, there has been no suggestion that TAG was a metalloprotein. However, here we establish by heteronuclear NMR and other spectroscopic methods that TAG binds 1 eq of Zn2+ extremely tightly. A family of refined NMR structures shows that 4 conserved residues contributed from the amino- and carboxyl-terminal regions of TAG (Cys4, His17, His175, and Cys179) form a Zn2+ binding site. The Zn2+ ion serves to tether the otherwise unstructured amino- and carboxyl-terminal regions of TAG. We propose that this unexpected “zinc snap” motif in the TAG family (CX12–17HX∼150HX3C) serves to stabilize the HhH domain thereby mimicking the functional role of protein-protein interactions in larger HhH superfamily members.
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A novel zinc snap motif conveys structural stability to 3-Methyladenine DNA glycosylase I
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, Chunyang Cao, James T StiversAbstract:The Escherichia coli 3-Methyladenine DNA glycosylase I (TAG) is a DNA repair enzyme that excises 3-Methyladenine in DNA and is the smallest member of the helix-hairpin-helix (HhH) superfamily of DNA glycosylases. Despite many studies over the last 25 years, there has been no suggestion that TAG was a metalloprotein. However, here we establish by heteronuclear NMR and other spectroscopic methods that TAG binds 1 eq of Zn2+ extremely tightly. A family of refined NMR structures shows that 4 conserved residues contributed from the amino- and carboxyl-terminal regions of TAG (Cys4, His17, His175, and Cys179) form a Zn2+ binding site. The Zn2+ ion serves to tether the otherwise unstructured amino- and carboxyl-terminal regions of TAG. We propose that this unexpected "zinc snap" motif in the TAG family (CX(12-17)HX(approximately 150)HX(3)C) serves to stabilize the HhH domain thereby mimicking the functional role of protein-protein interactions in larger HhH superfamily members.
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3 Methyladenine dna glycosylase i is an unexpected helix hairpin helix superfamily member
Nature Structural & Molecular Biology, 2002Co-Authors: Alexander C Drohat, Daniel J Krosky, Keehwan Kwon, James T StiversAbstract:The Escherichia coli enzyme 3-Methyladenine DNA glycosylase I (TAG) hydrolyzes the glycosidic bond of 3-Methyladenine (3-MeA) in DNA and is found in many bacteria and some higher eukaryotes. TAG shows little primary sequence identity with members of the well-known helix-hairpin-helix (HhH) superfamily of DNA repair glycosylases, which consists of AlkA, EndoIII, MutY and hOGG1. Unexpectedly, the threedimensional solution structure reported here reveals TAG as member of this superfamily. The restricted specificity of TAG for 3-MeA bases probably arises from its unique aromatic rich 3-MeA binding pocket and the absence of a catalytic aspartate that is present in all other HhH family members. Escherichia coli express two DNA glycosylases that hydrolytically cleave the glycosidic bond of alkylated purine bases in
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3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Nature structural biology, 2002Co-Authors: Alexander C Drohat, Daniel J Krosky, Keehwan Kwon, James T StiversAbstract:The Escherichia coli enzyme 3-Methyladenine DNA glycosylase I (TAG) hydrolyzes the glycosidic bond of 3-Methyladenine (3-MeA) in DNA and is found in many bacteria and some higher eukaryotes. TAG shows little primary sequence identity with members of the well-known helix-hairpin-helix (HhH) superfamily of DNA repair glycosylases, which consists of AlkA, EndoIII, MutY and hOGG1. Unexpectedly, the three-dimensional solution structure reported here reveals TAG as member of this superfamily. The restricted specificity of TAG for 3-MeA bases probably arises from its unique aromatic rich 3-MeA binding pocket and the absence of a catalytic aspartate that is present in all other HhH family members.
Keehwan Kwon - One of the best experts on this subject based on the ideXlab platform.
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solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3 Methyladenine dna glycosylase i
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, Alexander C Drohat, Yu Lin Jiang, James T StiversAbstract:Abstract The specific recognition mechanisms of DNA repair glycosylases that remove cationic alkylpurine bases in DNA are not well understood partly due to the absence of structures of these enzymes with their cognate bases. Here we report the solution structure of 3-Methyladenine DNA glycosylase I (TAG) in complex with its 3-Methyladenine (3-MeA) cognate base, and we have used chemical perturbation of the base in combination with mutagenesis of the enzyme to evaluate the role of hydrogen bonding and π-cation interactions in alkylated base recognition by this DNA repair enzyme. We find that TAG uses hydrogen bonding with heteroatoms on the base, van der Waals interactions with the 3-Me group, and conventional π-π stacking with a conserved Trp side chain to selectively bind neutral 3-MeA over the cationic form of the base. Discrimination against binding of the normal base adenine is derived from direct sensing of the 3-methyl group, leading to an induced-fit conformational change that engulfs the base in a box defined by five aromatic side chains. These findings indicate that base specific recognition by TAG does not involve strong π-cation interactions, and suggest a novel mechanism for alkylated base recognition and removal.
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a novel zinc snap motif conveys structural stability to 3 Methyladenine dna glycosylase i
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, James T StiversAbstract:Abstract The Escherichia coli 3-Methyladenine DNA glycosylase I (TAG) is a DNA repair enzyme that excises 3-Methyladenine in DNA and is the smallest member of the helix-hairpin-helix (HhH) superfamily of DNA glycosylases. Despite many studies over the last 25 years, there has been no suggestion that TAG was a metalloprotein. However, here we establish by heteronuclear NMR and other spectroscopic methods that TAG binds 1 eq of Zn2+ extremely tightly. A family of refined NMR structures shows that 4 conserved residues contributed from the amino- and carboxyl-terminal regions of TAG (Cys4, His17, His175, and Cys179) form a Zn2+ binding site. The Zn2+ ion serves to tether the otherwise unstructured amino- and carboxyl-terminal regions of TAG. We propose that this unexpected “zinc snap” motif in the TAG family (CX12–17HX∼150HX3C) serves to stabilize the HhH domain thereby mimicking the functional role of protein-protein interactions in larger HhH superfamily members.
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A novel zinc snap motif conveys structural stability to 3-Methyladenine DNA glycosylase I
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, Chunyang Cao, James T StiversAbstract:The Escherichia coli 3-Methyladenine DNA glycosylase I (TAG) is a DNA repair enzyme that excises 3-Methyladenine in DNA and is the smallest member of the helix-hairpin-helix (HhH) superfamily of DNA glycosylases. Despite many studies over the last 25 years, there has been no suggestion that TAG was a metalloprotein. However, here we establish by heteronuclear NMR and other spectroscopic methods that TAG binds 1 eq of Zn2+ extremely tightly. A family of refined NMR structures shows that 4 conserved residues contributed from the amino- and carboxyl-terminal regions of TAG (Cys4, His17, His175, and Cys179) form a Zn2+ binding site. The Zn2+ ion serves to tether the otherwise unstructured amino- and carboxyl-terminal regions of TAG. We propose that this unexpected "zinc snap" motif in the TAG family (CX(12-17)HX(approximately 150)HX(3)C) serves to stabilize the HhH domain thereby mimicking the functional role of protein-protein interactions in larger HhH superfamily members.
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3 Methyladenine dna glycosylase i is an unexpected helix hairpin helix superfamily member
Nature Structural & Molecular Biology, 2002Co-Authors: Alexander C Drohat, Daniel J Krosky, Keehwan Kwon, James T StiversAbstract:The Escherichia coli enzyme 3-Methyladenine DNA glycosylase I (TAG) hydrolyzes the glycosidic bond of 3-Methyladenine (3-MeA) in DNA and is found in many bacteria and some higher eukaryotes. TAG shows little primary sequence identity with members of the well-known helix-hairpin-helix (HhH) superfamily of DNA repair glycosylases, which consists of AlkA, EndoIII, MutY and hOGG1. Unexpectedly, the threedimensional solution structure reported here reveals TAG as member of this superfamily. The restricted specificity of TAG for 3-MeA bases probably arises from its unique aromatic rich 3-MeA binding pocket and the absence of a catalytic aspartate that is present in all other HhH family members. Escherichia coli express two DNA glycosylases that hydrolytically cleave the glycosidic bond of alkylated purine bases in
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3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Nature structural biology, 2002Co-Authors: Alexander C Drohat, Daniel J Krosky, Keehwan Kwon, James T StiversAbstract:The Escherichia coli enzyme 3-Methyladenine DNA glycosylase I (TAG) hydrolyzes the glycosidic bond of 3-Methyladenine (3-MeA) in DNA and is found in many bacteria and some higher eukaryotes. TAG shows little primary sequence identity with members of the well-known helix-hairpin-helix (HhH) superfamily of DNA repair glycosylases, which consists of AlkA, EndoIII, MutY and hOGG1. Unexpectedly, the three-dimensional solution structure reported here reveals TAG as member of this superfamily. The restricted specificity of TAG for 3-MeA bases probably arises from its unique aromatic rich 3-MeA binding pocket and the absence of a catalytic aspartate that is present in all other HhH family members.
Shabbir Ahmad - One of the best experts on this subject based on the ideXlab platform.
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quantum chemical and spectroscopic investigations of 3 Methyladenine
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2014Co-Authors: Mohammad Jane Alam, Shabbir AhmadAbstract:Abstract FTIR, FT-Raman and UV–Vis spectra of 3-Methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-Methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Quantum chemical and spectroscopic investigations of 3-Methyladenine
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 2014Co-Authors: Mohammad Jane Alam, Shabbir AhmadAbstract:FTIR, FT-Raman and UV-Vis spectra of 3-Methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-Methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory. ?? 2014 Elsevier B.V. All rights reserved.
Leona D Samson - One of the best experts on this subject based on the ideXlab platform.
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recognition and processing of a new repertoire of dna substrates by human 3 Methyladenine dna glycosylase aag
Biochemistry, 2009Co-Authors: James C Delaney, Maria Kartalou, Gondichatnahalli M Lingaraju, Ayelet Maorshoshani, John M Essigmann, Leona D SamsonAbstract:The human 3-Methyladenine DNA glycosylase (AAG) recognizes and excises a broad range of purines damaged by alkylation and oxidative damage, including 3-Methyladenine, 7-methylguanine, hypoxanthine (Hx), and 1,N6-ethenoadenine (eA). The crystal structures of AAG bound to eA have provided insights into the structural basis for substrate recognition, base excision, and exclusion of normal purines and pyrimidines from its substrate recognition pocket. In this study, we explore the substrate specificity of full-length and truncated Δ80AAG on a library of oligonucleotides containing structurally diverse base modifications. Substrate binding and base excision kinetics of AAG with 13 damaged oligonucleotides were examined. We found that AAG bound to a wide variety of purine and pyrimidine lesions but excised only a few of them. Single-turnover excision kinetics showed that in addition to the well-known eA and Hx substrates, 1-methylguanine (m1G) was also excised efficiently by AAG. Thus, along with eA and ethanoa...
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3 Methyladenine dna glycosylase deficient aag null mice display unexpected bone marrow alkylation resistance
Cancer Research, 2002Co-Authors: Richard Roth, Leona D SamsonAbstract:Most cells deficient in 3-Methyladenine (3MeA) DNA glycosylase become sensitive to the lethal and clastogenic effects of alkylating agents. Surprisingly, myeloid progenitor bone marrow (BM) cells derived from Aag −/− mice were more resistant than those from wild-type mice to the cytotoxic effects of several alkylating agents. Moreover, an alkylation-resistant phenotype was observed in vivo using the BM micronucleus assay as a measure of chromosome damage. Flow cytometry indicated that in vivo alkylation resistance in Aag null BM cells may be restricted to cells of the myeloid lineage. These results show that in particular cell types, the initiation of base excision repair is more lethal to the cell than leaving the damaged bases unrepaired by Aag.
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influence of dna structure on hypoxanthine and 1 n6 ethenoadenine removal by murine 3 Methyladenine dna glycosylase
Carcinogenesis, 2000Co-Authors: Michael D Wyatt, Leona D SamsonAbstract:: 3-Methyladenine DNA glycosylases initiate base excision repair by flipping the nucleotide bearing the target base out of double-stranded DNA into an active site pocket for glycosylic bond cleavage and base release. Substrate bases for the murine 3-Methyladenine DNA glycosylase (other than 3-Methyladenine) include hypoxanthine and 1,N(6)-ethenoadenine, two mutagenic adducts formed by both endogenous and exogenous agents. Using double-stranded DNA oligonucleotides containing damaged bases at specific sites, we studied the relative removal rates for these two adducts when located in different sequence contexts. One of the sequence contexts was an A:T tract, chosen because DNA secondary structure is known to change along the length of this tract, due to a progressive narrowing of the minor groove. Here we report that removal rates for hypoxanthine, but not for 1,N(6)-ethenoadenine, are dramatically affected by its location within the A:T tract. In addition, the removal rates of hypoxanthine and 1,N(6)-ethenoadenine when paired opposite thymine or cytosine were examined, and in each sequence context hypoxanthine removal decreased by at least 20-fold when paired opposite cytosine versus thymine. In contrast, 1, N(6)-ethenoadenine removal was unaffected by the identity of the opposing pyrimidine. We conclude that the removal of certain bases by the mouse 3-Methyladenine DNA glycosylase can be modulated by both adjacent and opposing sequence contexts. The influence of DNA sequence context upon DNA repair rates, such as those described here, may contribute to the creation of mutational hot spots in mammalian cells.
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3 Methyladenine dna glycosylases structure function and biological importance
BioEssays, 1999Co-Authors: Michael D Wyatt, Tom Ellenberger, James M Allan, Leona D SamsonAbstract:Summary The genome continuously suffers damage due to its reactivity with chemical and physical agents. Finding such damage in genomes (that can be several million to several billion nucleotide base pairs in size) is a seemingly daunting task. 3-Methyladenine DNA glycosylases can initiate the base excision repair (BER) of an extraordinarily wide range of substrate bases. The advantage of such broad substrate recognition is that these enzymes provide resistance to a wide variety of DNA damaging agents; however, under certain circumstances, the eclectic nature of these enzymes can confer some biological disadvantages. Solving the X-ray crystal structures of two 3-Methyladenine DNA glycosylases, and creating cells and animals altered for this activity, contributes to our understanding of their enzyme mechanism and how such enzymes influence the biological response of organisms to several different types of DNA damage. BioEssays 21:668‐676, 1999. r 1999 John Wiley & Sons, Inc.
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mammalian 3 Methyladenine dna glycosylase protects against the toxicity and clastogenicity of certain chemotherapeutic dna cross linking agents
Cancer Research, 1998Co-Authors: James M Allan, Michael D Wyatt, Bevin P Engelward, Andrew J Dreslin, Maria Tomasz, Leona D SamsonAbstract:DNA repair status is recognized as an important determinant of the clinical efficacy of cancer chemotherapy. To assess the role that a mammalian DNA glycosylase plays in modulating the toxicity and clastogenicity of the chemotherapeutic DNA cross-linking alkylating agents, we compared the sensitivity of wild-type murine cells to that of isogenic cells bearing homozygous null mutations in the 3-Methyladenine DNA glycosylase gene ( Aag ). We show that Aag protects against the toxic and clastogenic effects of 1,3-bis(2-chloroethyl)-1-nitrosourea and mitomycin C (MMC), as measured by cell killing, sister chromatid exchange, and chromosome aberrations. This protection is accompanied by suppression of apoptosis and a slightly reduced p53 response. Our results identify 3-Methyladenine DNA glycosylase-initiated base excision repair as a potentially important determinant of the clinical efficacy and, possibly, the carcinogenicity of these widely used chemotherapeutic agents. However, Aag does not contribute significantly to protection against the toxic and clastogenic effects of several chemotherapeutic nitrogen mustards (namely, mechlorethamine, melphalan, and chlorambucil), at least in the mouse embryonic stem cells used here. We also compare the Aag null phenotype with the Fanconi anemia phenotype, a human disorder characterized by cellular hypersensitivity to DNA cross-linking agents, including MMC. Although Aag null cells are sensitive to MMC-induced growth delay and cell cycle arrest, their sensitivity is modest compared to that of Fanconi anemia cells.
Alexander C Drohat - One of the best experts on this subject based on the ideXlab platform.
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solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3 Methyladenine dna glycosylase i
Journal of Biological Chemistry, 2003Co-Authors: Keehwan Kwon, Alexander C Drohat, Yu Lin Jiang, James T StiversAbstract:Abstract The specific recognition mechanisms of DNA repair glycosylases that remove cationic alkylpurine bases in DNA are not well understood partly due to the absence of structures of these enzymes with their cognate bases. Here we report the solution structure of 3-Methyladenine DNA glycosylase I (TAG) in complex with its 3-Methyladenine (3-MeA) cognate base, and we have used chemical perturbation of the base in combination with mutagenesis of the enzyme to evaluate the role of hydrogen bonding and π-cation interactions in alkylated base recognition by this DNA repair enzyme. We find that TAG uses hydrogen bonding with heteroatoms on the base, van der Waals interactions with the 3-Me group, and conventional π-π stacking with a conserved Trp side chain to selectively bind neutral 3-MeA over the cationic form of the base. Discrimination against binding of the normal base adenine is derived from direct sensing of the 3-methyl group, leading to an induced-fit conformational change that engulfs the base in a box defined by five aromatic side chains. These findings indicate that base specific recognition by TAG does not involve strong π-cation interactions, and suggest a novel mechanism for alkylated base recognition and removal.
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3 Methyladenine dna glycosylase i is an unexpected helix hairpin helix superfamily member
Nature Structural & Molecular Biology, 2002Co-Authors: Alexander C Drohat, Daniel J Krosky, Keehwan Kwon, James T StiversAbstract:The Escherichia coli enzyme 3-Methyladenine DNA glycosylase I (TAG) hydrolyzes the glycosidic bond of 3-Methyladenine (3-MeA) in DNA and is found in many bacteria and some higher eukaryotes. TAG shows little primary sequence identity with members of the well-known helix-hairpin-helix (HhH) superfamily of DNA repair glycosylases, which consists of AlkA, EndoIII, MutY and hOGG1. Unexpectedly, the threedimensional solution structure reported here reveals TAG as member of this superfamily. The restricted specificity of TAG for 3-MeA bases probably arises from its unique aromatic rich 3-MeA binding pocket and the absence of a catalytic aspartate that is present in all other HhH family members. Escherichia coli express two DNA glycosylases that hydrolytically cleave the glycosidic bond of alkylated purine bases in
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3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Nature structural biology, 2002Co-Authors: Alexander C Drohat, Daniel J Krosky, Keehwan Kwon, James T StiversAbstract:The Escherichia coli enzyme 3-Methyladenine DNA glycosylase I (TAG) hydrolyzes the glycosidic bond of 3-Methyladenine (3-MeA) in DNA and is found in many bacteria and some higher eukaryotes. TAG shows little primary sequence identity with members of the well-known helix-hairpin-helix (HhH) superfamily of DNA repair glycosylases, which consists of AlkA, EndoIII, MutY and hOGG1. Unexpectedly, the three-dimensional solution structure reported here reveals TAG as member of this superfamily. The restricted specificity of TAG for 3-MeA bases probably arises from its unique aromatic rich 3-MeA binding pocket and the absence of a catalytic aspartate that is present in all other HhH family members.
