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)

Abstract

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
Volume606
DOIs
Publication statusPublished - 2016 Sep 15

Fingerprint

Ribonuclease H
Exonucleases
Nucleotides
Processing
Pyrococcus furiosus
Poly T
Oligonucleotides
Thymidine
Crystal structure
poly(dA)
Proteins
Substrates

Keywords

  • A-form
  • Exonuclease
  • RNase H
  • ssDNA

ASJC Scopus subject areas

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

Cite this

Kim, J., Sambalkhundev, G. O., Kim, S., Son, J., Han, A. R., Ko, S. M., ... Lee, W. C. (2016). Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046. Archives of Biochemistry and Biophysics, 606, 143-150. https://doi.org/10.1016/j.abb.2016.08.001

Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046. / Kim, Junsoo; Sambalkhundev, Gerelt Od; Kim, Sulhee; Son, Jonghyeon; Han, Ah reum; Ko, Sul Min; Hwang, Kwang Yeon; Lee, Woo Cheol.

In: Archives of Biochemistry and Biophysics, Vol. 606, 15.09.2016, p. 143-150.

Research output: Contribution to journalArticle

Kim, Junsoo ; Sambalkhundev, Gerelt Od ; Kim, Sulhee ; Son, Jonghyeon ; Han, Ah reum ; Ko, Sul Min ; Hwang, Kwang Yeon ; Lee, Woo Cheol. / Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046. In: Archives of Biochemistry and Biophysics. 2016 ; Vol. 606. pp. 143-150.
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AB - 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.

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