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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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Structural comparison of NgTRF1561–681 and the DNA-binding domain of hTRF1. Proteins are represented by ribbon diagrams. NgTRF1561–681 is colored in green and the DNA-binding domain of hTRF1 is colored in yellow. The helices are numbered in sequence from N- to C-terminal. The X-ray crystal structures of the DNA-binding domain of hTRF1 in complex with telomeric DNA [PDB accession ID: 1W0T, (33)] was used for the structure of hTRF1.
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Figure 6: Structural comparison of NgTRF1561–681 and the DNA-binding domain of hTRF1. Proteins are represented by ribbon diagrams. NgTRF1561–681 is colored in green and the DNA-binding domain of hTRF1 is colored in yellow. The helices are numbered in sequence from N- to C-terminal. The X-ray crystal structures of the DNA-binding domain of hTRF1 in complex with telomeric DNA [PDB accession ID: 1W0T, (33)] was used for the structure of hTRF1.

Mentions: NgTRF1 is homologous to hTRF1. The full-length ORFs are 17% homologous, and there is 27% homology in the Myb-like domain alone (27). Although the DNA-binding domain of NgTRF1 has an additional C-terminal Myb-extension, the structures of the DNA-binding domains of the two proteins in complex with DNA are very similar, with an RMSD of 0.666 Å for the Cα atoms (Table 2, Figure 6). A hydrophobic core formed by helices 1, 2 and 3 is conserved in NgTRF1561–681 and hTRF1. In addition, helix 4 of NgTRF1561–681 also took part in the formation of the hydrophobic core. The hydrophobic interaction between helix 3 and helix 4 of NgTRF1561–681 made helix 3 longer than that of the DNA-binding domain of hTRF1 (Table 2). NgTRF1561–681 had four salt bridges. There were two unique ionic interactions in NgTRF1561–681, Arg-649 (in helix 4) with Glu-586 and with Glu-593 (in helix 1), further stabilizing the structure. The salt bridge between Arg-575 and Asp-618 links the N-terminal arm and helix 3, resulting in a broader area of interaction with the DNA. Arg-575 was not detected in the electron density map of DNA-unbound NgTRF1561–681, which suggested that the conformation of DNA-bound NgTRF1561–681 was stabilized further by this ionic interaction.Figure 6.


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)

Structural comparison of NgTRF1561–681 and the DNA-binding domain of hTRF1. Proteins are represented by ribbon diagrams. NgTRF1561–681 is colored in green and the DNA-binding domain of hTRF1 is colored in yellow. The helices are numbered in sequence from N- to C-terminal. The X-ray crystal structures of the DNA-binding domain of hTRF1 in complex with telomeric DNA [PDB accession ID: 1W0T, (33)] was used for the structure of hTRF1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 6: Structural comparison of NgTRF1561–681 and the DNA-binding domain of hTRF1. Proteins are represented by ribbon diagrams. NgTRF1561–681 is colored in green and the DNA-binding domain of hTRF1 is colored in yellow. The helices are numbered in sequence from N- to C-terminal. The X-ray crystal structures of the DNA-binding domain of hTRF1 in complex with telomeric DNA [PDB accession ID: 1W0T, (33)] was used for the structure of hTRF1.
Mentions: NgTRF1 is homologous to hTRF1. The full-length ORFs are 17% homologous, and there is 27% homology in the Myb-like domain alone (27). Although the DNA-binding domain of NgTRF1 has an additional C-terminal Myb-extension, the structures of the DNA-binding domains of the two proteins in complex with DNA are very similar, with an RMSD of 0.666 Å for the Cα atoms (Table 2, Figure 6). A hydrophobic core formed by helices 1, 2 and 3 is conserved in NgTRF1561–681 and hTRF1. In addition, helix 4 of NgTRF1561–681 also took part in the formation of the hydrophobic core. The hydrophobic interaction between helix 3 and helix 4 of NgTRF1561–681 made helix 3 longer than that of the DNA-binding domain of hTRF1 (Table 2). NgTRF1561–681 had four salt bridges. There were two unique ionic interactions in NgTRF1561–681, Arg-649 (in helix 4) with Glu-586 and with Glu-593 (in helix 1), further stabilizing the structure. The salt bridge between Arg-575 and Asp-618 links the N-terminal arm and helix 3, resulting in a broader area of interaction with the DNA. Arg-575 was not detected in the electron density map of DNA-unbound NgTRF1561–681, which suggested that the conformation of DNA-bound NgTRF1561–681 was stabilized further by this ionic interaction.Figure 6.

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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