TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Comment:involved in both strand cleavage and rejoining
Comment:reaction is Mg2+ dependent
Comment:catalytic mechanism of ssDNA cleavage in 1I7D_A: active site tyrosine forms a covalent linkage with the 5' phosphate of the scissile bond and conserved glutamate of TOPRIM domain donates a proton to the leaving 3' oxygen of the scissile bond
Structure:1CY4_A, E.coli Dna Topoisomerase I, bound with thymidine-5'-phosphate, contacts at 3.5A - View structure with Cn3D