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

Ko S, Jun SH, Bae H, Byun JS, Han W, Park H, Yang SW, Park SY, Jeon YH, Cheong C, Kim WT, Lee W, Cho HS - Nucleic Acids Res. (2008)

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea.

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 alpha-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).

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NMR spectrum and solution structure of NgTRF1561–681. (a) 1H-15N HSQC spectrum of 13C/15N labeled NgTRF1561–681. The spectrum was acquired at pH 7.0 and 298 K using a Bruker 600 MHz spectrometer. (b) The stereo plots of the backbone atoms of the 20 lowest-energy structures of NgTRF1561–681 are superimposed with respect to the average structure of the defined residues of 582–659 (N, Cα,C′,O).
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Figure 2: NMR spectrum and solution structure of NgTRF1561–681. (a) 1H-15N HSQC spectrum of 13C/15N labeled NgTRF1561–681. The spectrum was acquired at pH 7.0 and 298 K using a Bruker 600 MHz spectrometer. (b) The stereo plots of the backbone atoms of the 20 lowest-energy structures of NgTRF1561–681 are superimposed with respect to the average structure of the defined residues of 582–659 (N, Cα,C′,O).

Mentions: We first analyzed NgTRF1561–681 using NMR spectroscopy. All peptide backbone resonance assignments of NgTRF1561–681 were completed with the exception of the 3 N-terminal residues, which were not resolved due to resonance overlap (Figure 2a). Residues 582–660 adopt a well-defined tertiary structure and it was refined to a root mean square deviation (RMSD) of 0.86 Å for backbone atoms. Most of the Φ, Ψ angles of the final structures were appropriately distributed in the Ramachandran plot and the structural statistics are presented in Table 1.Figure 2.


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

Ko S, Jun SH, Bae H, Byun JS, Han W, Park H, Yang SW, Park SY, Jeon YH, Cheong C, Kim WT, Lee W, Cho HS - Nucleic Acids Res. (2008)

NMR spectrum and solution structure of NgTRF1561–681. (a) 1H-15N HSQC spectrum of 13C/15N labeled NgTRF1561–681. The spectrum was acquired at pH 7.0 and 298 K using a Bruker 600 MHz spectrometer. (b) The stereo plots of the backbone atoms of the 20 lowest-energy structures of NgTRF1561–681 are superimposed with respect to the average structure of the defined residues of 582–659 (N, Cα,C′,O).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2377444&req=5

Figure 2: NMR spectrum and solution structure of NgTRF1561–681. (a) 1H-15N HSQC spectrum of 13C/15N labeled NgTRF1561–681. The spectrum was acquired at pH 7.0 and 298 K using a Bruker 600 MHz spectrometer. (b) The stereo plots of the backbone atoms of the 20 lowest-energy structures of NgTRF1561–681 are superimposed with respect to the average structure of the defined residues of 582–659 (N, Cα,C′,O).
Mentions: We first analyzed NgTRF1561–681 using NMR spectroscopy. All peptide backbone resonance assignments of NgTRF1561–681 were completed with the exception of the 3 N-terminal residues, which were not resolved due to resonance overlap (Figure 2a). Residues 582–660 adopt a well-defined tertiary structure and it was refined to a root mean square deviation (RMSD) of 0.86 Å for backbone atoms. Most of the Φ, Ψ angles of the final structures were appropriately distributed in the Ramachandran plot and the structural statistics are presented in Table 1.Figure 2.

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea.

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 alpha-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).

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