Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046

Junsoo Kim, Gerelt Od Sambalkhundev, Sulhee Kim, Jonghyeon Son, Ah reum Han, Sul Min Ko, Kwang Yeon Hwang, Woo Cheol Lee

Research output: Contribution to journalArticle

1 Citation (Scopus)


RNase H fold protein PF2046 of Pyrococcus furiosus is a 3′-5′ ssDNA exonuclease that cleaves after the second nucleotide from the 3′ end of ssDNA and prefers poly-dT over poly-dA as a substrate. In our crystal structure of PF2046 complexed with an oligonucleotide of four thymidine nucleotides (dT4), PF2046 accommodates dT4 tightly in a groove and imposes steric hindrance on dT4 mainly by Phe220 such that dT4 assumes the A-form. As poly-dA prefer B-form due to the stereochemical restrictions, the A-form ssDNA binding by PF2046 should disfavor the processing of poly-dA. Phe220 variants display reduced activity toward poly-dA and the A-form appears to be a prerequisite for the processing by PF2046.

Original languageEnglish
Pages (from-to)143-150
Number of pages8
JournalArchives of Biochemistry and Biophysics
Publication statusPublished - 2016 Sep 15


  • A-form
  • Exonuclease
  • RNase H
  • ssDNA

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Medicine(all)
  • Molecular Biology

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  • Cite this

    Kim, J., Sambalkhundev, G. O., Kim, S., Son, J., Han, A. R., Ko, S. M., Hwang, K. Y., & Lee, W. C. (2016). Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046. Archives of Biochemistry and Biophysics, 606, 143-150.