Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus

Suhng Wook Kim, Dong Uk Kim, Jin Kwang Kim, Lin Woo Kang, Hyun Soo Cho

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)356-361
Number of pages6
JournalInternational Journal of Biological Macromolecules
Volume42
Issue number4
DOIs
Publication statusPublished - 2008 May 1

Fingerprint

Pyrococcus furiosus
Exonucleases
Thumb
DNA-Directed DNA Polymerase
Polymerization
Crystal structure
Structural analysis
Carrier concentration
Electrons
Polymerase Chain Reaction
Enzymes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Economics and Econometrics
  • Energy(all)

Cite this

Kim, Suhng Wook ; Kim, Dong Uk ; Kim, Jin Kwang ; Kang, Lin Woo ; Cho, Hyun Soo. / Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus. In: International Journal of Biological Macromolecules. 2008 ; Vol. 42, No. 4. pp. 356-361.
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abstract = "We have determined a 2.6 {\AA} 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.",
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Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus. / Kim, Suhng Wook; Kim, Dong Uk; Kim, Jin Kwang; Kang, Lin Woo; Cho, Hyun Soo.

In: International Journal of Biological Macromolecules, Vol. 42, No. 4, 01.05.2008, p. 356-361.

Research output: Contribution to journalArticle

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