Solution structure of the DNA binding domain of rice telomere binding protein RTBP

Sunggeon Ko, Eun Young Yu, Joon Shin, Hyun Hee Yoo, Toshiyuki Tanaka, Woo Taek Kim, Hyun Soo Cho, Weontae Lee, In Kwon Chung

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

RTBP1 is a rice telomeric protein that binds to the duplex array of TTTAGGG repeats at chromosome ends. The DNA binding domain of RTBP1 contains a Myb-type DNA binding motif and a highly conserved C-terminal Myb extension that is unique to plant telomeric proteins. Using an electrophoretic mobility shift assay, we identified the C-terminal 110-amino acid region (RTBP1 506-615) as the minimal telomeric DNA binding domain, suggesting that the Myb extension is required for binding plant telomeric DNA. Like other telomeric proteins such as human TRF1 and yeast Rap1, RTBP1 induced a DNA bending in the telomeric repeat sequence, suggesting that RTBP1 may play a role in establishing and/or maintaining an active telomere configuration in vivo. To elucidate the DNA binding mode of RTBP1, we determined the three-dimensional structure of RTBP1506-615 in solution by NMR spectroscopy. The overall structure of RTBP1506-615 is composed of four α-helices and stabilized by three hydrophobic patches. The second and third helices in RTBP1 form a helix-turn-helix motif that interacts directly with DNA. The fourth helix located in the Myb extension is essential for binding to telomeric DNA via stabilization of the overall structure of the RTBP1 DNA binding domain. When DNA bound to RTBP1506-615, large chemical shift perturbations were induced in the N-terminal arm, helix 3, and the loop between helices 3 and 4. These results suggest that helix 3 functions as a sequence-specific recognition helix while the N-terminal arm stabilizes the DNA binding.

Original languageEnglish
Pages (from-to)827-838
Number of pages12
JournalBiochemistry
Volume48
Issue number5
DOIs
Publication statusPublished - 2009 Feb 10

Fingerprint

Telomere-Binding Proteins
DNA
Helix-Turn-Helix Motifs
Plant DNA
Oryza
Plant Proteins
Nucleotide Motifs
Telomere
Electrophoretic Mobility Shift Assay
Electrophoretic mobility
Proteins
Chemical shift
Chromosomes
Magnetic Resonance Spectroscopy
Yeast
Yeasts
Nuclear magnetic resonance spectroscopy

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

Ko, Sunggeon ; Yu, Eun Young ; Shin, Joon ; Yoo, Hyun Hee ; Tanaka, Toshiyuki ; Kim, Woo Taek ; Cho, Hyun Soo ; Lee, Weontae ; Chung, In Kwon. / Solution structure of the DNA binding domain of rice telomere binding protein RTBP. In: Biochemistry. 2009 ; Vol. 48, No. 5. pp. 827-838.
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Solution structure of the DNA binding domain of rice telomere binding protein RTBP. / Ko, Sunggeon; Yu, Eun Young; Shin, Joon; Yoo, Hyun Hee; Tanaka, Toshiyuki; Kim, Woo Taek; Cho, Hyun Soo; Lee, Weontae; Chung, In Kwon.

In: Biochemistry, Vol. 48, No. 5, 10.02.2009, p. 827-838.

Research output: Contribution to journalArticle

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AU - Ko, Sunggeon

AU - Yu, Eun Young

AU - Shin, Joon

AU - Yoo, Hyun Hee

AU - Tanaka, Toshiyuki

AU - Kim, Woo Taek

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AU - Chung, In Kwon

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N2 - RTBP1 is a rice telomeric protein that binds to the duplex array of TTTAGGG repeats at chromosome ends. The DNA binding domain of RTBP1 contains a Myb-type DNA binding motif and a highly conserved C-terminal Myb extension that is unique to plant telomeric proteins. Using an electrophoretic mobility shift assay, we identified the C-terminal 110-amino acid region (RTBP1 506-615) as the minimal telomeric DNA binding domain, suggesting that the Myb extension is required for binding plant telomeric DNA. Like other telomeric proteins such as human TRF1 and yeast Rap1, RTBP1 induced a DNA bending in the telomeric repeat sequence, suggesting that RTBP1 may play a role in establishing and/or maintaining an active telomere configuration in vivo. To elucidate the DNA binding mode of RTBP1, we determined the three-dimensional structure of RTBP1506-615 in solution by NMR spectroscopy. The overall structure of RTBP1506-615 is composed of four α-helices and stabilized by three hydrophobic patches. The second and third helices in RTBP1 form a helix-turn-helix motif that interacts directly with DNA. The fourth helix located in the Myb extension is essential for binding to telomeric DNA via stabilization of the overall structure of the RTBP1 DNA binding domain. When DNA bound to RTBP1506-615, large chemical shift perturbations were induced in the N-terminal arm, helix 3, and the loop between helices 3 and 4. These results suggest that helix 3 functions as a sequence-specific recognition helix while the N-terminal arm stabilizes the DNA binding.

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