Resolving the relationships of resolving enzymes.

H junction-resolving enzymes are metal ion-dependent endonucleases that recognize and cleave four-way DNA junctions arising during recombination (reviewed in ref. 1). Examples include RuvC in eubacteria (2, 3), Cce1 in fungal mitochondria (4), Hjc in archaea (5, 6), and three enzymes in bacteriophage [RusA (7), T4 endonuclease VII (8), and T7 endonuclease I (9, 10)]. These six nucleases display no detectable sequence similarity with standard techniques, and the crystal structures of RuvC (11), T4 endonuclease VII (12), and T7 endonuclease I (S. E. V. Phillips and D.M.J.L., unpublished observations) are topologically dissimilar. This plethora of seemingly unrelated proteins carrying out essentially similar roles in different organisms has been a source of some puzzlement, as it has suggested that the evolution of Holliday junction resolution had occurred relatively recently, postdating the divergence of the three domains of life. This was at odds with the generally accepted view that homologous recombination is a fundamental process present in virtually all life forms and that strand-exchange proteins RecAyRad51 are universal. This paradox has been resolved by the identification of the pox viral junctionresolving enzyme (13), based on weak sequence similarity to both Cce1 and RuvC, and allows us to apply Occam’s Razor to simplify the resolving enzyme family tree. Garcia et al. made the connection between the eubacterial, pox, and mitochondrial resolving enzymes by using RuvC as a probe for the program PSI BLAST (14). This allowed identification of weak homologs in the pox viruses, including protein A22 in vaccinia. Subsequent searches with these proteins picked up the similarity with the fungal mitochondrial resolving enzymes. The vaccinia A22 protein was subsequently expressed in Escherichia coli and was shown to be a functional resolving enzyme in vitro (13). By approaching from another direction, we came to the same conclusion by defining four conserved motifs in the fungal resolving enzymes (Fig. 1A), containing residues identified by site-directed mutagenesis as essential for substrate binding or catalysis. These motifs were used to search for homologous proteins (using the program MOTIFSEARCH, GCG Wisconsin package), leading to the identification of the pox viral A22 homologs, which in turn allowed the connection with RuvC. The pox virus enzymes are slightly more similar to the fungal than to the eubacterial enzymes, with 31:51 (% identityy% similarity) for the entomopoxyYdc2 pair, and 28:39 for the entomopoxyRuvC pair. The mitochondrial enzymes, ranging in size from 258 to 353 residues, are signifi-