PDBsum entry: 2ckx

Nuclear protein

PDB id: 2ckx

Contents

Protein chain

83 a.a. *

Waters ×99

* Residue conservation analysis

PDB id:

2ckx

Name:

Nuclear protein

Title:

Crystal structure of ngtrf1, double-stranded telomeric repeat binding factor from nicotiana tabacum.

Structure:

Telomere binding protein tbp1. Chain: a. Fragment: telomeric DNA binding domain, residues 578-660. Synonym: ngtrf1. Engineered: yes

Source:

Nicotiana tabacum. Tobacco. Organism_taxid: 4097. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.210 R-free: 0.232

Authors:

J.-S.Byun, H.-S.Cho

Key ref:

S.Ko et al. (2008). Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins. Nucleic Acids Res, 36, 2739-2755. PubMed id: 18367475 DOI: 10.1093/nar/gkn030

Date:

24-Apr-06 Release date: 29-May-07

Protein chain

Q84ZU4  (Q84ZU4_NICGU) -  Telomere binding protein TBP1

Seq: 681 a.a.

Struc: 83 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription (1 term)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1093/nar/gkn030

Nucleic Acids Res 36:2739-2755 (2008)

PubMed id: 18367475

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

S.Ko, S.H.Jun, H.Bae, J.S.Byun, W.Han, H.Park, S.W.Yang, S.Y.Park, Y.H.Jeon, C.Cheong, W.T.Kim, W.Lee, H.S.Cho.

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).