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Crystal structure of an archaebacterial DNA polymerase
Y Zhao1, D Jeruzalmi, I Moarefi
1Laboratories of Molecular Biophysics The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
Structure (London, England : 1993)
|November 5, 1999
Summary
The crystal structure of a heat-stable Pol II DNA polymerase reveals similarities to Pol I polymerases in its catalytic core but distinct surrounding structures. This suggests conserved DNA replication mechanisms alongside unique features in Pol II family polymerases.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Biology
Background:
- DNA polymerases (Pol II family) are crucial for eukaryotic chromosomal replication, distinct from the well-studied Pol I family.
- The archaeal Desulfurococcus strain Tok DNA polymerase (D. Tok Pol) is a heat-stable Pol II member.
Purpose of the Study:
- To determine the crystal structure of D. Tok Pol.
- To compare its structural features with other DNA polymerases, particularly Pol I and RB69.
- To infer functional and evolutionary relationships within DNA polymerase families.
Main Methods:
- X-ray crystallography to determine the 3D structure of D. Tok Pol at 2.4 A resolution.
Main Results:
- D. Tok Pol shares structural similarity with bacteriophage RB69 DNA polymerase, despite low sequence identity.
- The catalytic core (palm subdomain) of D. Tok Pol resembles that of Pol I polymerases.
- The proofreading exonuclease domain is positioned similarly to RB69 but differently from Pol I polymerases.
- An N-terminal domain shows similarity to RNA-binding domains, conserved in eukaryotic Pol delta and epsilon.
Conclusions:
- DNA binding and product extrusion mechanisms are likely conserved between Pol II and Pol I polymerases.
- The proofreading exonuclease transit mechanism must differ between Pol II and Pol I.
- The RNA-binding domain suggests potential RNA interactions for Pol II family members.