TOPRIM - A CONSERVED CATALYTIC DOMAIN IN TYPE IA AND II TOPOISOMERASES, DNAG-TYPE PRIMASES, OLD FAMILY NUCLEASES AND RECR PROTEINS

Iterative profile searches and structural modeling show that bacterial DnaG-type primases, small primase-like proteins from bacteria and arc haea, type IA and type It topoisomerases, bacterial and archaeal nucle ases of the OLD family and bacterial DNA repair proteins of the RecR/M family contain a common domain, designated Toprim (topoisomerase-prim ase) domain. The domain consists of similar to 100 amino acids and has two conserved motifs, one of which centers at a conserved glutamate a nd the other one at two conserved aspartates (DxD), Examination of the structure of Topo IA and Topo II and modeling of the Toprim domains o f the primases reveal a compact beta/alpha fold, with the conserved ne gatively charged residues juxtaposed, and inserts seen in Topo IA and Topo II. The conserved glutamate may act as a general base in nucleoti de polymerization by primases and in strand rejoining by topoisomerase s and as a general acid in strand cleavage by topoisomerases and nucle ases, The role of this glutamate in catalysis is supported by site-dir ected mutagenesis data on primases and Topo IA. The DxD motif may coor dinate Mg2+ that is required for the activity of all Toprim-containing enzymes. The common ancestor of all life forms could encode a prototy pe Toprim enzyme that might have had both nucleotidyl transferase and polynucleotide cleaving activity.