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 journalArticlepeer-review

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 Sept 15

Bibliographical note

Funding Information:
We thank supporting staff of beamline BL1A of the Photon Factory (Tsukuba, Japan) for the help with data collection. This research was supported by Basic Science Research Program through the gs2:National Research Foundation of Korea funded by the Ministry of Education ( NRF-2013R1A1A2059835 ] to WCL. WCL and KYH were supported by the Korea University grants.

Publisher Copyright:
© 2016 Elsevier Inc.


  • A-form
  • Exonuclease
  • RNase H
  • ssDNA

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology


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