Crystal structure of an archaebacterial DNA polymerase

Background: Members of the Pol II family of DNA polymerases are responsible for chromosomal replication in eukaryotes, and carry out highly processive DNA replication when attached to ring-shaped processivity clamps. The sequ ences of Pol II polymerases are distinct from those of members of the well- studied Pol I family of DNA polymerases. The DNA polymerase from the archae bacterium Desulfurococcus strain Tok (D. Tok Pol) is a member of the Pol II family that retains catalytic activity at elevated temperatures. Results: The crystal structure of D. Tok Pol has been determined at 2.4 Ang strom resolution. The architecture of this Pol II type DNA polymerase resem bles that of the DNA polymerase from the bacteriophage RB69, with which it shares less than similar to 20% sequence identity. As in RB69, the central catalytic region of the DNA polymerase is located within the 'palm' subdoma in and is strikingly similar in structure to the corresponding regions of P ol I type DNA polymerases. The structural scaffold that surrounds the catal ytic core in D. Tok Pol is unrelated in structure to that of Pol I type pol ymerases. The 3'-5' proofreading exonuclease domain of D. Tok Pol resembles the corresponding domains of RB69 Pol and Pol I type DNA polymerases. The exonuclease domain in D. Tok Pol is located in the same position relative t o the polymerase domain as seen in RB69, and on the opposite side of the pa lm subdomain compared to its location in Pol I type polymerases. The N-term inal domain of D. Tok Pol has structural similarity to RNA-binding domains. Sequence alignments suggest that this domain is conserved in the eukaryoti c DNA polymerases delta and epsilon. Conclusions: The structure of D. Tok Pol confirms that the modes of binding of the template and extrusion of newly synthesized duplex DNA are likely t o be similar in both Pol II and Pol I type DNA polymerases. However, the me chanism by which the newly synthesized product transits in and out of the p roofreading exonuclease domain has to be quite different. The discovery of a domain that seems to be an RNA-binding module raises the possibility that Pol II family members interact with RNA.