Interacts with mus81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks and nicked Holliday junctions. May be required in mitosis for the processing of stalled or collapsed replication fork intermediates. May be required in meiosis for the repair of meiosis-specific double strand breaks subsequent to single-end invasion (SEI). Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Interacts with mus81. S.pombe appears to be critically dependent on the mus81-eme1 endonuclease for the resolution of meiotic crossovers. This may be due to the absence of an alternate pathway for crossover resolution such as the MSH4-MSH5 pathway which exists in S.cerevisiae and other eukaryotes. Belongs to the EME1/MMS4 family.