Saccharomyces cerevisiae Spo11 protein (Spo11p) is thought to generate the DNA double-strand breaks (DSBs) that initiate homologous recombination during meiosis. Spo11p is related to a subunit of archaebacterial topoisomerase VI and appears to cleave DNA through a topoisomerase-like transesterase mechanism. In this work, we used the crystal structure of a fragment of topoisomerase VI to model the Spo11p structure and to identify amino acid residues in yeast Spo11p potentially involved in DSB catalysis and/or DNA binding. These residues were mutated to determine which are critical for Spo11p function in vivo. Mutation of Glu-233 or Asp-288, which lie in a conserved structural motif called the Toprim domain, abolished meiotic recombination. These Toprim domain residues have been implicated in binding a metal ion cofactor in topoisomerases and bacterial primases, supporting the idea that DNA cleavage by Spo11p is Mg 2؉ dependent. Mutations at an invariant arginine (Arg-131) within a second conserved structural motif known as the 5Y-CAP domain, as well as three other mutations (E235A, F260R, and D290A), caused marked changes in the DSB pattern at a recombination hotspot, suggesting that Spo11p contributes directly to the choice of DNA cleavage site. Finally, certain DSB-defective mutant alleles generated in this study conferred a semidominant negative phenotype but only when Spo11p activity was partially compromised by the presence of an epitope tag. These results are consistent with a multimeric structure for Spo11p in vivo but may also indicate that the amount of Spo11 protein is not a limiting factor for DSB formation in normal cells.Homologous recombination during meiosis in Saccharomyces cerevisiae proceeds via the formation and subsequent repair of DNA double-strand breaks (DSBs) (reviewed in references 24 and 38). Formation of these DSBs requires the products of at least 10 genes, including SPO11. The Spo11 protein (Spo11p) was found covalently linked to the 5Ј-strand termini of DSBs in certain mutants (e.g., rad50S) that are defective for the normal 5Ј-to-3Ј nucleolytic processing of DSB ends (23), and Spo11p shares sequence similarity with a subunit of an archaebacterial topoisomerase (6). Based on these observations, it is thought that Spo11p is the catalytic subunit of the meiotic DNA cleaving activity and that it cuts DNA by a topoisomerase-like transesterification reaction. The role of Spo11p in promoting meiotic recombination initiation is widely conserved, as functional homologs have been characterized in fungi, plants, and animals (3,10,11,16,18,26,30,31,35,43).It is likely that all of the archaebacterial Spo11p homologs function as type II topoisomerases, but topoisomerase activity has been directly demonstrated only for the enzyme from Sulfolobus shibatae (5,8). Because the amino acid sequence of this topoisomerase is unlike the previously known eukaryotic and prokaryotic type II enzymes, it was named topoisomerase VI to distinguish it from these proteins (6). Topoisomerase VI is an A 2 B 2 heterot...