We have determined a 2.6 Å resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and β-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.
|Number of pages||6|
|Journal||International Journal of Biological Macromolecules|
|Publication status||Published - 2008 May 1|
Bibliographical noteFunding Information:
We thank Drs. Sun-Sin Cha and Kyunghwa Kim for assistance at beamline 6B and 4MX of the Pohang Light Source. This work was supported by Korea Research Foundation grants from the Korean Government (R08-2004-000-10403-02-004), by Korea Science and Engineering Foundation (KOSEF) grant (R112000078010010), by Korea Research Foundation Grant funded by the Korean Government (KRF-2004-005-J04502), and by a grant (Code # 20070501034003) from BioGreen 21 Program, Rural Development Administration, in Republic of Korea.
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology
- Economics and Econometrics