Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA.
In order to gain insights into the mechaism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.
Perry
Kay
K
Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
Mondragón
Alfonso
A
D000595:Amino Acid Sequence; D019611:Archaeoglobus fulgidus / Q000201:enzymology; D001120:Arginine / Q000737:chemistry; D001665:Binding Sites; D002384:Catalysis; D004247:DNA / Q000737:chemistry; D004264:DNA Topoisomerases, Type I / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology* / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid
D004277:DNA, Single-Stranded; D009841:Oligonucleotides; D004247:DNA; D001120:Arginine; D004264:DNA Topoisomerases, Type I