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

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

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.

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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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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DO - 10.1016/j.abb.2016.08.001

M3 - Article

C2 - 27495739

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

Bibliographical note

Keywords

ASJC Scopus subject areas

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