A newly identified, essential catalytic residue in a critical secondary structure element in the integrase family of site-specific recombinases is conserved in a similar element in eucaryotic type IB topoisomerases

The integrase family of site-specific recombinases catalyzes conservative r earrangements between defined segments of DNA. A highly conserved tetrad (R HRY) of catalytic residues is essential for this process. This tetrad is di spersed in two motifs in the linear sequence, but is configured appropriate ly in the catalytic pocket to execute the strand cleavage and rejoining rea ctions. A third conserved motif has been identified in the Xer subgroup of the integrase family. Mutational analysis of 12 conserved residues in this motif in the XerD protein from Salmonella typhimurium led to the identifica tion of an essential fifth catalytic residue (lysine 172) which is implicat ed in strand cleavage or exchange. This lysine residue occupies part of the turn of an antiparallel beta-hairpin which forms one side of the catalytic cleft in XerD, and is found at similar positions among evolutionarily dive rse integrase family members. Related antiparallel beta-hairpins are presen t in eucaryotic type IB topoisomerase enzymes which also contain a critical lysine residue in the turn of the hairpin. Ln both the integrase family an d eucaryotic type IB topoisomerases, the catalytic lysine residues are in c lose contact with the substrates and may play similar roles in influencing the reactivity of the phosphotyrosine intermediates formed during reactions catalyzed by both enzymes. (C) 1999 Academic Press.