Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA

Yunseok Heo; Jae Hyun Park; Jongmin Kim; Jeongmin Han; Ji Hye Yun; Weontae Lee

doi:10.1016/j.bbrc.2020.09.094

Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA

Yunseok Heo, Jae Hyun Park, Jongmin Kim, Jeongmin Han, Ji Hye Yun, Weontae Lee

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

4 Citations (Scopus)

Abstract

The SWI/SNF chromatin remodeling complex plays important roles in gene regulation and it is classified as the SWI/SNF complex in yeast and BAF complex in vertebrates. BAF57, one of the subunits that forms the chromatin remodeling complex core, is well conserved in the BAF complex of vertebrates, which is replaced by bap111 in the Drosophila BAP complex and does not have a counterpart in the yeast SWI/SNF complex. This suggests that BAF57 is a key component of the chromatin remodeling complex in higher eukaryotes. BAF57 contains a HMG domain, which is widely distributed among various proteins and functions as a DNA binding motif. Most proteins with HMG domain bind to four-way junction (4WJ) DNA. Here, we report the crystal structure of the HMG domain of BAF57 (BAF57^HMG) at a resolution of 2.55 Å. The structure consists of three α-helices and adopts an L-shaped form. The overall structure is stabilized by a hydrophobic core, which is formed by hydrophobic residues. The binding affinity between BAF57^HMG and 4WJ DNA is determined as a 295.83 ± 1.05 nM using a fluorescence quenching assay, and the structure revealed 4WJ DNA binding site of BAF57^HMG. Our data will serve structural basis in understanding the roles of BAF57 during chromatin remodeling process.

Original language	English
Pages (from-to)	919-924
Number of pages	6
Journal	Biochemical and Biophysical Research Communications
Volume	533
Issue number	4
DOIs	https://doi.org/10.1016/j.bbrc.2020.09.094
Publication status	Published - 2020 Dec 17

Bibliographical note

Funding Information:
This work was supported by the Mid-career Researcher Program ( NRF-2017R1A2B2008483 , NRF-2019M3E5D6063903 , and NRF-2017M3A9F6029753 to W. Lee, and NRF-20161A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea (NRF) and the Brain Korea Plus (BK+) program (Y. Heo). We thank the staff of the beamline at the Pohang Accelerator Laboratory (PAL) for assistance during X-ray data collection.

Publisher Copyright:
© 2020

All Science Journal Classification (ASJC) codes

Biophysics
Biochemistry
Molecular Biology
Cell Biology

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10.1016/j.bbrc.2020.09.094

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title = "Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA",

abstract = "The SWI/SNF chromatin remodeling complex plays important roles in gene regulation and it is classified as the SWI/SNF complex in yeast and BAF complex in vertebrates. BAF57, one of the subunits that forms the chromatin remodeling complex core, is well conserved in the BAF complex of vertebrates, which is replaced by bap111 in the Drosophila BAP complex and does not have a counterpart in the yeast SWI/SNF complex. This suggests that BAF57 is a key component of the chromatin remodeling complex in higher eukaryotes. BAF57 contains a HMG domain, which is widely distributed among various proteins and functions as a DNA binding motif. Most proteins with HMG domain bind to four-way junction (4WJ) DNA. Here, we report the crystal structure of the HMG domain of BAF57 (BAF57HMG) at a resolution of 2.55 {\AA}. The structure consists of three α-helices and adopts an L-shaped form. The overall structure is stabilized by a hydrophobic core, which is formed by hydrophobic residues. The binding affinity between BAF57HMG and 4WJ DNA is determined as a 295.83 ± 1.05 nM using a fluorescence quenching assay, and the structure revealed 4WJ DNA binding site of BAF57HMG. Our data will serve structural basis in understanding the roles of BAF57 during chromatin remodeling process.",

author = "Yunseok Heo and Park, {Jae Hyun} and Jongmin Kim and Jeongmin Han and Yun, {Ji Hye} and Weontae Lee",

note = "Funding Information: This work was supported by the Mid-career Researcher Program ( NRF-2017R1A2B2008483 , NRF-2019M3E5D6063903 , and NRF-2017M3A9F6029753 to W. Lee, and NRF-20161A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea (NRF) and the Brain Korea Plus (BK+) program (Y. Heo). We thank the staff of the beamline at the Pohang Accelerator Laboratory (PAL) for assistance during X-ray data collection. Publisher Copyright: {\textcopyright} 2020",

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AU - Heo, Yunseok

AU - Park, Jae Hyun

AU - Kim, Jongmin

AU - Han, Jeongmin

AU - Yun, Ji Hye

AU - Lee, Weontae

N1 - Funding Information: This work was supported by the Mid-career Researcher Program ( NRF-2017R1A2B2008483 , NRF-2019M3E5D6063903 , and NRF-2017M3A9F6029753 to W. Lee, and NRF-20161A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea (NRF) and the Brain Korea Plus (BK+) program (Y. Heo). We thank the staff of the beamline at the Pohang Accelerator Laboratory (PAL) for assistance during X-ray data collection. Publisher Copyright: © 2020

PY - 2020/12/17

Y1 - 2020/12/17

N2 - The SWI/SNF chromatin remodeling complex plays important roles in gene regulation and it is classified as the SWI/SNF complex in yeast and BAF complex in vertebrates. BAF57, one of the subunits that forms the chromatin remodeling complex core, is well conserved in the BAF complex of vertebrates, which is replaced by bap111 in the Drosophila BAP complex and does not have a counterpart in the yeast SWI/SNF complex. This suggests that BAF57 is a key component of the chromatin remodeling complex in higher eukaryotes. BAF57 contains a HMG domain, which is widely distributed among various proteins and functions as a DNA binding motif. Most proteins with HMG domain bind to four-way junction (4WJ) DNA. Here, we report the crystal structure of the HMG domain of BAF57 (BAF57HMG) at a resolution of 2.55 Å. The structure consists of three α-helices and adopts an L-shaped form. The overall structure is stabilized by a hydrophobic core, which is formed by hydrophobic residues. The binding affinity between BAF57HMG and 4WJ DNA is determined as a 295.83 ± 1.05 nM using a fluorescence quenching assay, and the structure revealed 4WJ DNA binding site of BAF57HMG. Our data will serve structural basis in understanding the roles of BAF57 during chromatin remodeling process.

AB - The SWI/SNF chromatin remodeling complex plays important roles in gene regulation and it is classified as the SWI/SNF complex in yeast and BAF complex in vertebrates. BAF57, one of the subunits that forms the chromatin remodeling complex core, is well conserved in the BAF complex of vertebrates, which is replaced by bap111 in the Drosophila BAP complex and does not have a counterpart in the yeast SWI/SNF complex. This suggests that BAF57 is a key component of the chromatin remodeling complex in higher eukaryotes. BAF57 contains a HMG domain, which is widely distributed among various proteins and functions as a DNA binding motif. Most proteins with HMG domain bind to four-way junction (4WJ) DNA. Here, we report the crystal structure of the HMG domain of BAF57 (BAF57HMG) at a resolution of 2.55 Å. The structure consists of three α-helices and adopts an L-shaped form. The overall structure is stabilized by a hydrophobic core, which is formed by hydrophobic residues. The binding affinity between BAF57HMG and 4WJ DNA is determined as a 295.83 ± 1.05 nM using a fluorescence quenching assay, and the structure revealed 4WJ DNA binding site of BAF57HMG. Our data will serve structural basis in understanding the roles of BAF57 during chromatin remodeling process.

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EP - 924

JO - Biochemical and Biophysical Research Communications

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Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA

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