A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases

Primases synthesize short RNA strands on single-stranded DNA templates, the reby generating the hybrid duplexes required for the initiation of synthesi s by DNA polymerases. We present the crystal structure of the catalytic uni t of a primase enzyme, that of a similar to 320 residue fragment of Escheri chia coli primase, determined at 2.9 Angstrom resolution. Central to the ca talytic unit is a TOPRlM domain that is strikingly similar in its structure to that of corresponding domains in DNA topoisomerases, but is unrelated t o the catalytic centers of other DNA or RNA polymerases. The catalytic doma in of primase is crescent-shaped, and the concave face of the crescent is p redicted to accommodate about 10 base-pairs of RNA-DNA duplex in a loose in teraction, thereby limiting processivity. (C) 2000 Academic Press.