Protein Name

Bifunctional DNA primase-polymerase


Sulfolobus islandicus (archaea)

Biological Context

DNA replication is a process required in all organisms before any of its cells divide into daughter cells. DNA replication involves the accurate duplication of the vast amounts of genetic information encoded in the DNA. It requires the splitting of the double stranded parent DNA into two single strands, unwinding of the parent strands and creation of two new strands using the two parent strands as templates. DNA polymerase and primase are the primary enzymes required for DNA replication within a cell. Primase synthesizes an initial short strand of oligonucleotides, called a primer. DNA polymerase adds one deoxyribonucleotide at a time in the 5'-3' direction to this pre-existing primer to extend it. Though polymerases and primases exist as two independent enzymes, they have recently been identified in the form of a combined primase-polymerase (prim-pol) domain in replicases from archaeal plasmids.

Structure Description


The above structure is that of the N-terminal domain of one such replicase, pRN1 from Sulfolobus islandicus. An important feature of the crystal structure is the presence of a central concave depression lined by conserved residues. The 3 acidic residues in the center of this depression along with an adjacent histidine form the active site of the prim-pol domain and are responsible for both the DNA polymerase and the primase activity. A basic ridge opposite the active site forms the DNA binding domain. Another feature is the zinc-binding stem. This stem forms one groove with the DNA binding domain which allows the DNA template strand to reach the active site. The stem is also in close contact with the active site residues and forms the groove that may allow the incoming nucleotides to come in proximity with the template strand. This domain structure is unrelated to that of known primases and polymerases and forms a new family.

Protein Data Bank (PDB)



  • Lipps, G. Weinzierl, A.O. Von Scheven, G. Buchen, C. Cramer, P.; "Structure of a bifunctional DNA primase-polymerase"; Nat.Struct.Mol.Biol.; (2004) 11:157-162 PubMed:14730355.


author: Ashwini Patil

Japanese version:PDB:1RNI