SIMILARITIES AND DIFFERENCES AMONG 105 MEMBERS OF THE INT FAMILY OF SITE-SPECIFIC RECOMBINASES

Alignments of 105 site-specific recombinases belonging to the Int fami ly of proteins identified extended areas of similarity and three types of structural differences, In addition to the previously recognized c onservation of the tetrad R-H-R-Y, located in boxes I and II, several newly identified sequence patches include charged amino acids that are highly conserved and a specific pattern of buried residues contributi ng to the overall protein fold, With some notable exceptions, unconser ved regions correspond to loops in the crystal structures of the catal ytic domains of lambda Int (Int cl 70) and HP1 Int (HPC) and of the re combinases XerD and Cre, Two structured regions also harbor some prono unced differences, The first comprises beta-sheets 4 and 5, alpha-heli x D and the adjacent loop connecting it to alpha-helix E: two Ints of phages infecting thermophilic bacteria are missing this region altoget her; the crystal structures of HPC, XerD and Cre reveal a lack of beta -sheets 4 and 5; Cre displays two additional beta-sheets following alp ha-helix D; five recombinases carry large insertions, The second invol ves the catalytic tyrosine and is seen in a comparison of the four cry stal structures, The yeast recombinases can theoretically be fitted to the Int fold, but the overall differences, involving changes in spaci ng as well as in motif structure, are more substantial than seen in mo st other proteins. The phenotypes of mutations compiled from several p roteins are correlated with the available structural information and s tructure-function relationships are discussed, In addition, a few prok aryotic and eukaryotic enzymes with partial homology with the Int fami ly of recombinases may be distantly related, either through divergent or convergent evolution. These include a restriction enzyme and a subg roup of eukaryotic RNA helicases (D-E-A-D proteins).