Metal ion interactions in the DNA cleavage/ligation active site of human topoisomerase IIalpha.
Human topoisomerase IIalpha utilizes a two-metal-ion mechanism for DNA cleavage. One of the metal ions (M(1)(2+)) is believed to make a critical interaction with the 3'-bridging atom of the scissile phosphate, while the other (M(2)(2+)) is believed to interact with a nonbridging oxygen of the scissile phosphate. Based on structural and mutagenesis studies of prokaryotic nucleic acid enzymes, it has been proposed that the active site divalent metal ions interact with type II topoisomerases through a series of conserved acidic amino acid residues. The homologous residues in human topoisomerase IIalpha are E461, D541, D543, and D545. To address the validity of these assignments and to delineate interactions between individual amino acids and M(1)(2+) and M(2)(2+), we individually mutated each of these acidic amino acid residues in topoisomerase IIalpha to either cysteine or alanine. Mutant enzymes displayed a marked loss of catalytic and DNA cleavage activity as well as a reduced affinity for divalent metal ions. Additional experiments determined the ability of wild-type and mutant topoisomerase IIalpha enzymes to cleave an oligonucleotide substrate that contained a sulfur atom in place of the 3'-bridging oxygen of the scissile phosphate in the presence of Mg2+, Mn2+, or Ca2+. On the basis of the results of these studies, we conclude that the four acidic amino acid residues interact with metal ions in the DNA cleavage/ligation active site of topoisomerase IIalpha. Furthermore, we propose that M(1)(2+) interacts with E461, D543, and D545 and M(2)(2+) interacts with E461 and D541.
Deweese
Joseph E
JE
Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
Guengerich
F Peter
FP
Burgin
Alex B
AB
Osheroff
Neil
N
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000951:Antigens, Neoplasm / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D020134:Catalytic Domain / Q000235:genetics; D002413:Cations, Divalent / Q000378:metabolism; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D017931:DNA Primers / Q000235:genetics; D004250:DNA Topoisomerases, Type II / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D066298:In Vitro Techniques; D007700:Kinetics; D008670:Metals / Q000378:metabolism; D008956:Models, Chemical; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000235:genetics / Q000378:metabolism; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D000951:Antigens, Neoplasm; D002413:Cations, Divalent; D017931:DNA Primers; D004268:DNA-Binding Proteins; D008670:Metals; D009838:Oligodeoxyribonucleotides; D011994:Recombinant Proteins; D004247:DNA; D004250:DNA Topoisomerases, Type II
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