, Volume 23, Issue 1, pp 161–172 | Cite as

Elucidating functions of DP1 and DP2 subunits from the Thermococcus kodakarensis family D DNA polymerase

  • Natsuki Takashima
  • Sonoko IshinoEmail author
  • Keisuke Oki
  • Mika Takafuji
  • Takeshi Yamagami
  • Ryotaro Matsuo
  • Kouta Mayanagi
  • Yoshizumi IshinoEmail author
Original Paper


DNA polymerase D (PolD), originally discovered in Pyrococcus furiosus, has no sequence homology with any other DNA polymerase family. Genes encoding PolD are found in most of archaea, except for those archaea in the Crenarchaeota phylum. PolD is composed of two proteins: DP1 and DP2. To date, the 3D structure of the PolD heteromeric complex is yet to be determined. In this study, we established a method that prepared highly purified PolD from Thermococcus kodakarensis, and purified DP1 and DP2 proteins formed a stable complex in solution. An intrinsically disordered region was identified in the N-terminal region of DP1, but the static light scattering analysis provided a reasonable molecular weight of DP1. In addition, PolD forms as a complex of DP1 and DP2 in a 1:1 ratio. Electron microscope single particle analysis supported this composition of PolD. Both proteins play an important role in DNA synthesis activity and in 3′–5′ degradation activity. DP1 has extremely low affinity for DNA, while DP2 is mainly responsible for DNA binding. Our work will provide insight and the means to further understand PolD structure and the molecular mechanism of this archaea-specific DNA polymerase.


Thermococcus kodakarensis DNA polymerase DNA replication Archaea Euryarchaeota 



Static light scattering


Circular dichroism


Electron microscopy


Right angle light scattering



The authors thank Ryo Ugawa (Research Promotion Unit, Medical Institute of Bioregulation, Kyushu University) for technical assistance.


This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant numbers JP21113005, JP23310152, and JP26242075 to Y. I., JP16H01410 to K.M., and JP18K05442 to S.I.). K.M. was also supported by JST PRESTO (JPMJPR12L9)

Compliance with ethical standards

Conflict of interest

None declared.

Supplementary material

792_2018_1070_MOESM1_ESM.pdf (3.3 mb)
Supplementary material 1 (PDF 3416 kb)


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Copyright information

© Springer Japan KK, part of Springer Nature 2018

Authors and Affiliations

  • Natsuki Takashima
    • 1
  • Sonoko Ishino
    • 1
    Email author
  • Keisuke Oki
    • 1
  • Mika Takafuji
    • 1
  • Takeshi Yamagami
    • 1
  • Ryotaro Matsuo
    • 3
  • Kouta Mayanagi
    • 2
  • Yoshizumi Ishino
    • 1
    Email author
  1. 1.Graduate School of Bioresource and Bioenvironmental SciencesKyushu UniversityFukuokaJapan
  2. 2.Medical Institute of BioregulationKyushu UniversityFukuokaJapan
  3. 3.Division of Malvern PanalyticalSpectris Co., LtdTokyoJapan

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