Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins

Sunggeon Ko; Sung Hoon Jun; Hansol Bae; Jung Sue Byun; Woong Han; Heeyoung Park; Seong Wook Yang; Sam Yong Park; Young Ho Jeon; Chaejoon Cheong; Woo Taek Kim; Weontae Lee; Hyun Soo Cho

doi:10.1093/nar/gkn030

Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins

Sunggeon Ko, Sung Hoon Jun, Hansol Bae, Jung Sue Byun, Woong Han, Heeyoung Park, Seong Wook Yang, Sam Yong Park, Young Ho Jeon, Chaejoon Cheong, Woo Taek Kim, Weontae Lee, Hyun Soo Cho

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Abstract

Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561-681 (NgTRF1^561-681), and was composed of 4 α-helices. We also determined the structure of NgTRF1^561-681 bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1^561-681 with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1^561-681, may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)_n.

Original language	English
Pages (from-to)	2739-2755
Number of pages	17
Journal	Nucleic acids research
Volume	36
Issue number	8
DOIs	https://doi.org/10.1093/nar/gkn030
Publication status	Published - 2008 May

Bibliographical note

Funding Information:
We thank Dr Sun-Sin Cha and Ghyung Hwa Kim for assistance at beamline 6B and 4MX of Pohang Light Source. This work was supported in part by grant from the Korea Research Foundation by the Korean Government (MOEHRD, Basic Research Promotion Fund) (KRF-2007-314-C00274 to H.S.C.), the Korea Science and Engineering Foundation Grantz (No R112000078010010 to H.S.C.), the NRL program of MOST NRDP (M1-0203-00-0020 to W.L.), the Korea Science and Engineering Foundation (KOSEF) through the Protein Network Research Center at Yonsei University (R112000078010010), the Plant Diversity Research Center (21st Century Frontier Research Program funded by the Ministry of Science and Technology of the Korean government to W.T.K.) and the Plant Metabolism Research Center at Kyung Hee University (Science Research Center Project No. R11-2000-081 from the Korea Science and Engineering Foundation to W.T.K.). This work was also supported by the Basic Science Research Program (C.C.) from the Ministry of Science and Technology of the Republic of Korea and by the NMR Research Program (Y.H.J.) from the Korea Basic Science Institute. S.-G.K., H.B., J.-S B., W.H. and H.P. were recipients of Brain Korea 21 postdoctoral or graduate student scholarship. Funding to pay the Open Access publication charges for this article was provided by the Protein Network Research Center at Yonsei University.

All Science Journal Classification (ASJC) codes

Genetics

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10.1093/nar/gkn030

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title = "Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins",

abstract = "Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561-681 (NgTRF1561-681), and was composed of 4 α-helices. We also determined the structure of NgTRF1561-681 bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1561-681 with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1561-681, may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)n.",

author = "Sunggeon Ko and Jun, {Sung Hoon} and Hansol Bae and Byun, {Jung Sue} and Woong Han and Heeyoung Park and Yang, {Seong Wook} and Park, {Sam Yong} and Jeon, {Young Ho} and Chaejoon Cheong and Kim, {Woo Taek} and Weontae Lee and Cho, {Hyun Soo}",

note = "Funding Information: We thank Dr Sun-Sin Cha and Ghyung Hwa Kim for assistance at beamline 6B and 4MX of Pohang Light Source. This work was supported in part by grant from the Korea Research Foundation by the Korean Government (MOEHRD, Basic Research Promotion Fund) (KRF-2007-314-C00274 to H.S.C.), the Korea Science and Engineering Foundation Grantz (No R112000078010010 to H.S.C.), the NRL program of MOST NRDP (M1-0203-00-0020 to W.L.), the Korea Science and Engineering Foundation (KOSEF) through the Protein Network Research Center at Yonsei University (R112000078010010), the Plant Diversity Research Center (21st Century Frontier Research Program funded by the Ministry of Science and Technology of the Korean government to W.T.K.) and the Plant Metabolism Research Center at Kyung Hee University (Science Research Center Project No. R11-2000-081 from the Korea Science and Engineering Foundation to W.T.K.). This work was also supported by the Basic Science Research Program (C.C.) from the Ministry of Science and Technology of the Republic of Korea and by the NMR Research Program (Y.H.J.) from the Korea Basic Science Institute. S.-G.K., H.B., J.-S B., W.H. and H.P. were recipients of Brain Korea 21 postdoctoral or graduate student scholarship. Funding to pay the Open Access publication charges for this article was provided by the Protein Network Research Center at Yonsei University.",

year = "2008",

month = may,

doi = "10.1093/nar/gkn030",

language = "English",

volume = "36",

pages = "2739--2755",

journal = "Nucleic Acids Research",

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T1 - Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins

AU - Ko, Sunggeon

AU - Jun, Sung Hoon

AU - Bae, Hansol

AU - Byun, Jung Sue

AU - Han, Woong

AU - Park, Heeyoung

AU - Yang, Seong Wook

AU - Park, Sam Yong

AU - Jeon, Young Ho

AU - Cheong, Chaejoon

AU - Kim, Woo Taek

AU - Lee, Weontae

AU - Cho, Hyun Soo

N1 - Funding Information: We thank Dr Sun-Sin Cha and Ghyung Hwa Kim for assistance at beamline 6B and 4MX of Pohang Light Source. This work was supported in part by grant from the Korea Research Foundation by the Korean Government (MOEHRD, Basic Research Promotion Fund) (KRF-2007-314-C00274 to H.S.C.), the Korea Science and Engineering Foundation Grantz (No R112000078010010 to H.S.C.), the NRL program of MOST NRDP (M1-0203-00-0020 to W.L.), the Korea Science and Engineering Foundation (KOSEF) through the Protein Network Research Center at Yonsei University (R112000078010010), the Plant Diversity Research Center (21st Century Frontier Research Program funded by the Ministry of Science and Technology of the Korean government to W.T.K.) and the Plant Metabolism Research Center at Kyung Hee University (Science Research Center Project No. R11-2000-081 from the Korea Science and Engineering Foundation to W.T.K.). This work was also supported by the Basic Science Research Program (C.C.) from the Ministry of Science and Technology of the Republic of Korea and by the NMR Research Program (Y.H.J.) from the Korea Basic Science Institute. S.-G.K., H.B., J.-S B., W.H. and H.P. were recipients of Brain Korea 21 postdoctoral or graduate student scholarship. Funding to pay the Open Access publication charges for this article was provided by the Protein Network Research Center at Yonsei University.

PY - 2008/5

Y1 - 2008/5

N2 - Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561-681 (NgTRF1561-681), and was composed of 4 α-helices. We also determined the structure of NgTRF1561-681 bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1561-681 with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1561-681, may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)n.

AB - Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561-681 (NgTRF1561-681), and was composed of 4 α-helices. We also determined the structure of NgTRF1561-681 bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1561-681 with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1561-681, may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)n.

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Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins

Abstract

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