Abstract
Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Adenine / analogs & derivatives
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Adenine / metabolism
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AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase
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Binding Sites
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Cross-Linking Reagents / chemistry
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Crystallography, X-Ray
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DNA / chemistry
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DNA / metabolism*
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DNA Damage
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DNA Repair
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DNA Repair Enzymes / chemistry*
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DNA Repair Enzymes / metabolism
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DNA-Binding Proteins / chemistry
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DNA-Binding Proteins / metabolism
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Dioxygenases / chemistry*
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Dioxygenases / metabolism*
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Escherichia coli Proteins / chemistry*
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Escherichia coli Proteins / metabolism*
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Humans
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Mixed Function Oxygenases / chemistry*
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Mixed Function Oxygenases / metabolism*
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Models, Molecular
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Protein Binding
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RNA / metabolism*
Substances
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Cross-Linking Reagents
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DNA-Binding Proteins
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Escherichia coli Proteins
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1-methyladenine
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RNA
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DNA
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Mixed Function Oxygenases
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Dioxygenases
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AlkB protein, E coli
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ALKBH2 protein, human
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AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase
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DNA Repair Enzymes
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Adenine
Associated data
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PDB/3BI3
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PDB/3BIE
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PDB/3BKZ
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PDB/3BTX
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PDB/3BTY
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PDB/3BTZ
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PDB/3BU0
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PDB/3BUC