Conservation of Structure and Mechanism between Eukaryotic Topoisomerase I and Site-Specific Recombinases

Abstract

Vaccinia DNA topoisomerase breaks and rejoins DNA strands through a DNA-(3'-phosphotyrosyl)-enzyme intermediate. A C-terminal catalytic domain, Topo(81-314), suffices for transesterification chemistry. The domain contains a constellation of five amino acids, conserved in all eukaryotic type IB topoisomerases, that catalyzes attack of the tyrosine nucleophile on the scissile phosphate. The structure of the catalytic domain, consisting of ten alpha helices and a three-strand beta sheet, resembles the catalytic domains of site-specific recombinases that act via a topoisomerase IB-like mechanism. The topoisomerase catalytic pentad is conserved in the tertiary structures of the recombinases despite scant sequence similarity overall. This implies that the catalytic domains of type IB topoisomerases and recombinases derive from a common ancestral strand transferase.

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

“…Our present observations as well as our previous study of BaP DE-2 dG adducts (15) underline recent progress in the understanding of the molecular contacts between topoisomerases and their DNA substrates (7,8,15,(48)(49)(50), and the potential of such structures to elucidate the molecular interactions of various ligands, including carcinogenic adducts as well as antibacterial and anticancer drugs.…”

Cre Mutants with Altered DNA Binding Properties

“…The flexible loop of integrase should reorganize toward an ␣-helix, which sterically adjusts the catalytic triad to the conformation found with HP1, XerD or, Cre. This should result in a triple helical DNA binding motif which is common for all integrases and underlines recent results with eukaryotic topoisomerases and site-specific recombinases that suggest that the catalytic domains of these proteins derive from a common ancestral strand transferase (45).…”

An unusual type IB topoisomerase from African trypanosomes

“…A final intriguing possibility afforded by an A 2 B 2 structure is the opportunity for domain swapping to support recombinase activity. As noted above, there are close similarities between these classes of enzymes, indeed most recombinases have topoisomerase activity and conversely type IB enzymes may resolve Holiday structures (25,33).…”

“…First, each subunit contributes essential and highly conserved catalytic residues that characterize both the type IB topoisomerases and the tyrosine recombinases (T. brucei Arg 377L , Lys 415L , Arg 471L , His 514L and Tyr 233S ; ref. 25). Like other IBs, the T. brucei topoisomerase has a Lys at 468L, not the His seen in recombinases (26).…”

“…There is some phylogenetic evidence to support the latter. As noted above, the tyrosine recombinases and type IB topoisomerases share mechanistic, structural and (to a lesser extent) sequence similarities (25). This has led to the concept that these two enzyme classes share a common ancestral catalytic domain that fused over time with different N-terminal domains (31).…”