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

doi:10.1016/j.abb.2016.08.001

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

Department of Biosystems and Biotechnology

Research output: Contribution to journal › Article › peer-review

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 language	English
Pages (from-to)	143-150
Number of pages	8
Journal	Archives of Biochemistry and Biophysics
Volume	606
DOIs	https://doi.org/10.1016/j.abb.2016.08.001
Publication status	Published - 2016 Sept 15

Keywords

A-form
Exonuclease
RNase H
ssDNA

ASJC Scopus subject areas

Biophysics
Biochemistry
Molecular Biology

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10.1016/j.abb.2016.08.001

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title = "Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046",

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.",

keywords = "A-form, Exonuclease, RNase H, ssDNA",

author = "Junsoo Kim and Sambalkhundev, {Gerelt Od} and Sulhee Kim and Jonghyeon Son and Han, {Ah reum} and Ko, {Sul Min} and Hwang, {Kwang Yeon} and Lee, {Woo Cheol}",

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: {\textcopyright} 2016 Elsevier Inc.",

year = "2016",

month = sep,

day = "15",

doi = "10.1016/j.abb.2016.08.001",

language = "English",

volume = "606",

pages = "143--150",

journal = "Archives of Biochemistry and Biophysics",

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T1 - Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046

AU - Kim, Junsoo

AU - Sambalkhundev, Gerelt Od

AU - Kim, Sulhee

AU - Son, Jonghyeon

AU - Han, Ah reum

AU - Ko, Sul Min

AU - Hwang, Kwang Yeon

AU - Lee, Woo Cheol

N1 - 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.

PY - 2016/9/15

Y1 - 2016/9/15

N2 - 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.

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.

KW - A-form

KW - Exonuclease

KW - RNase H

KW - ssDNA

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U2 - 10.1016/j.abb.2016.08.001

DO - 10.1016/j.abb.2016.08.001

M3 - Article

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AN - SCOPUS:84982823912

SN - 0003-9861

VL - 606

SP - 143

EP - 150

JO - Archives of Biochemistry and Biophysics

JF - Archives of Biochemistry and Biophysics

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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