Solution structure of the arabidopsis thaliana telomeric repeat-binding protein DNA binding domain: A new fold with an additional C-terminal helix

Shih Che Sue, Hsin Hao Hsiao, Ben C.P. Chung, Ying Hsien Cheng, Kuang Lung Hsueh, Chung Mong Chen, Chia Hsing Ho, Tai Huang Huang

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1464-560), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1464-560 binds to a 13-mer DNA duplex containing a single repeat of an A. thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a KD∼10-6-10-7 M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1464-560 is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1464-560 induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.

Original languageEnglish
Pages (from-to)72-85
Number of pages14
JournalJournal of Molecular Biology
Volume356
Issue number1
DOIs
Publication statusPublished - 2006 Feb 10

Fingerprint

DNA-Binding Proteins
Arabidopsis
DNA
Telomere-Binding Proteins
Amino Acids
Nucleotide Motifs
Electrophoretic Mobility Shift Assay
Amides
Magnetic Resonance Spectroscopy
Proteins

Keywords

  • AtTRP
  • Myb domain
  • NMR structure
  • Telomere binding protein

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Solution structure of the arabidopsis thaliana telomeric repeat-binding protein DNA binding domain : A new fold with an additional C-terminal helix. / Sue, Shih Che; Hsiao, Hsin Hao; Chung, Ben C.P.; Cheng, Ying Hsien; Hsueh, Kuang Lung; Chen, Chung Mong; Ho, Chia Hsing; Huang, Tai Huang.

In: Journal of Molecular Biology, Vol. 356, No. 1, 10.02.2006, p. 72-85.

Research output: Contribution to journalArticle

Sue, Shih Che ; Hsiao, Hsin Hao ; Chung, Ben C.P. ; Cheng, Ying Hsien ; Hsueh, Kuang Lung ; Chen, Chung Mong ; Ho, Chia Hsing ; Huang, Tai Huang. / Solution structure of the arabidopsis thaliana telomeric repeat-binding protein DNA binding domain : A new fold with an additional C-terminal helix. In: Journal of Molecular Biology. 2006 ; Vol. 356, No. 1. pp. 72-85.
@article{7cf977c7068a4f9aa2b9e39082f4c1b1,
title = "Solution structure of the arabidopsis thaliana telomeric repeat-binding protein DNA binding domain: A new fold with an additional C-terminal helix",
abstract = "The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1464-560), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1464-560 binds to a 13-mer DNA duplex containing a single repeat of an A. thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a KD∼10-6-10-7 M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1464-560 is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1464-560 induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.",
keywords = "AtTRP, Myb domain, NMR structure, Telomere binding protein",
author = "Sue, {Shih Che} and Hsiao, {Hsin Hao} and Chung, {Ben C.P.} and Cheng, {Ying Hsien} and Hsueh, {Kuang Lung} and Chen, {Chung Mong} and Ho, {Chia Hsing} and Huang, {Tai Huang}",
year = "2006",
month = "2",
day = "10",
doi = "10.1016/j.jmb.2005.11.009",
language = "English",
volume = "356",
pages = "72--85",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - Solution structure of the arabidopsis thaliana telomeric repeat-binding protein DNA binding domain

T2 - A new fold with an additional C-terminal helix

AU - Sue, Shih Che

AU - Hsiao, Hsin Hao

AU - Chung, Ben C.P.

AU - Cheng, Ying Hsien

AU - Hsueh, Kuang Lung

AU - Chen, Chung Mong

AU - Ho, Chia Hsing

AU - Huang, Tai Huang

PY - 2006/2/10

Y1 - 2006/2/10

N2 - The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1464-560), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1464-560 binds to a 13-mer DNA duplex containing a single repeat of an A. thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a KD∼10-6-10-7 M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1464-560 is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1464-560 induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.

AB - The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1464-560), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1464-560 binds to a 13-mer DNA duplex containing a single repeat of an A. thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a KD∼10-6-10-7 M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1464-560 is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1464-560 induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.

KW - AtTRP

KW - Myb domain

KW - NMR structure

KW - Telomere binding protein

UR - http://www.scopus.com/inward/record.url?scp=30344457013&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=30344457013&partnerID=8YFLogxK

U2 - 10.1016/j.jmb.2005.11.009

DO - 10.1016/j.jmb.2005.11.009

M3 - Article

C2 - 16337232

AN - SCOPUS:30344457013

VL - 356

SP - 72

EP - 85

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 1

ER -