PDBsum entry 2aje

DNA binding protein

PDB id: 2aje

Contents

Protein chain

97 a.a. *

* Residue conservation analysis

PDB id:

2aje

Name:

DNA binding protein

Title:

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

Structure:

Telomere repeat-binding protein. Chain: a. Fragment: telomeric binding domain. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

15 models

Authors:

H.H.Hsiao,S.C.Sue,B.C.Chung,Y.H.Cheng,T.H.Huang

Key ref:

S.C.Sue et al. (2006). Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain: a new fold with an additional C-terminal helix. J Mol Biol, 356, 72-85. PubMed id: 16337232 DOI: 10.1016/j.jmb.2005.11.009

Date:

01-Aug-05 Release date: 04-Jul-06

Protein chain

Q8L7L8  (TRP1_ARATH) -  Telomere repeat-binding protein 1 from Arabidopsis thaliana

Seq: 578 a.a.

Struc: 97 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2005.11.009

J Mol Biol 356:72-85 (2006)

PubMed id: 16337232

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

S.C.Sue, H.H.Hsiao, B.C.Chung, Y.H.Cheng, K.L.Hsueh, C.M.Chen, C.H.Ho, T.H.Huang.

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 (AtTRP1(464-560)), 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 AtTRP1(464-560) 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 K(D) approximately 10(-6)-10(-7) M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1(464-560) 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 AtTRP1(464-560) 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.

Selected figure(s)

Figure 6.
Figure 6. Identification of DNA-binding site. (a) Sequence variation with DNA binding induced chemical shift changes, Click to view the MathML source- [0?wchp=dGLbVtb-zSkWA] , of the AtTRP1[464-560] amide resonances, where Dd[NH] and Dd[N] is the chemical-shift difference for NH and 15N, respectively. (b) A schematic representation of the AtTRP1[464-560] structure. The red rods represent the helices. (c) Electrostatic charge potential on the surface of AtTRP1[464-560]. (d) The spatial locations of the DNA-perturbed residues of AtTRP1[464-560]. The magnitudes of the DNA binding-induced chemical shifts are color-coded as follow: red, Dd>0.6 ppm; orange, 0.6 >Dd> 0.4 ppm; yellow, 0.4>Dd>0.2 ppm; white, 0.02>Dd>0 ppm. Proline residues, or residues with amide resonances that cannot be observed, are colored dark grey. All structures are shown in the same orientation as in (b). (e) A model structure of AtTRP1[464-560] bound to a double-stranded telomeric DNA (sequence 5'-TAGGGTTTAGGGT-3'). The backbone of the protein molecule is shown as a yellow rope and the four helices are shown as red cylinders. The green sticks indicate residues with significant chemical shift perturbations attained upon binding to DNA. Grey and blue sticks represent the backbones of the two strands of DNA molecules, and the negatively charged phosphate group, respectively.

Figure 7.
Figure 7. Comparison of the structure of AtTRP1[464-560] with other Myb domains. (a) Sequence alignment of the Myb domain in the double-stranded telomere repeat-binding proteins (dsTRPs). Abbreviations are: hTRF1, human TRF1; hTRF2, human TRF2; mTRF1, murine TRF1; c-Myb R1, the first Myb domain of c-Myb; c-Myb R2, the second Myb domain of c-Myb; c-Myb R3, the third Myb domain of c-Myb; Rap1 sc1, Saccharomyces cerevisiae Rap1 subdomain 1; Rap1 sc2, S. cerevisiae Rap1 subdomain 2; RTBP1, Rice TRP; and AtTRP1, A. thaliana TRP. The helical regions are underlined and colored red. (b) Superposition of the first three helices of AtTRP1[464-560] (yellow) and the cMyb R1 domain (orange). (c) Superposition of the first three helices and the structure of hTRF1 (red).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 72-85) copyright 2006.

Figures were selected by an automated process.