title: AlkB demethylases flip out in different ways.
abstract: Aberrant methylations in DNA are repaired by base excision repair (BER) and direct repair by a methyltransferase or by an oxidative demethylase of the AlkB type. Yang et al. [Nature 452 (2008) 961-966] have now solved the crystal structure of AlkB and human AlkB homolog 2 (hABH2) in complex with DNA using an ingenious crosslinking strategy to stabilize the DNA-protein complex. AlkB proteins have similar catalytic domains, but different DNA recognition motifs. Whereas AlkB mainly makes contact with the damaged strand, hABH2 makes numerous contacts with both strands. hABH2 flips out the damaged base and fills the vacant space by a hydrophobic amino acid residue similar to DNA glycosylases, essentially without distorting the double helix structure. In contrast, AlkB squeezes together the bases flanking the flipped-out base to maintain the base stack. This unprecedented flipping mechanism and the differences between AlkB and hABH2 in contacting the DNA strands explain their preferences for single stranded- and double stranded DNA, respectively.
authors: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons Gate 1, Trondheim, Norway.
authors: Ottar
authors: O
authors: Sundheim
authors: Vivi A
authors: VA
authors: Talstad
authors: Cathrine Broberg
authors: CB
authors: Vågbø
authors: Geir
authors: G
authors: Slupphaug
authors: Hans E
authors: HE
authors: Krokan
mesh_terms: D000071499:AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase; D000595:Amino Acid Sequence; D003432:Cross-Linking Reagents / Q000494:pharmacology; D004247:DNA / Q000235:genetics*; D004249:DNA Damage; D019175:DNA Methylation; D004260:DNA Repair; D045643:DNA Repair Enzymes / Q000737:chemistry* / Q000502:physiology; D049308:Dioxygenases / Q000737:chemistry* / Q000502:physiology; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006899:Mixed Function Oxygenases / Q000737:chemistry*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D017386:Sequence Homology, Amino Acid
chemical_list: D003432:Cross-Linking Reagents; D029968:Escherichia coli Proteins; D012313:RNA; D004247:DNA; D006899:Mixed Function Oxygenases; D049308:Dioxygenases; C466427:AlkB protein, E coli; C486440:ALKBH2 protein, human; D000071499:AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase; D045643:DNA Repair Enzymes