Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.
We have determined a 2.6A 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 beta-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.
Kim
Suhng Wook
SW
Department of Clinical Laboratory Science, College of Health Sciences, Korea University, Seoul 136-703, Republic of Korea.
Kim
Dong-Uk
DU
Kim
Jin Kwang
JK
Kang
Lin-Woo
LW
Cho
Hyun-Soo
HS
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray / Q000379:methods; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D020027:Pyrococcus furiosus / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
C072146:Pfu DNA polymerase; D004259:DNA-Directed DNA Polymerase