spacer
spacer

PDBsum entry 2aje

Go to PDB code: 
protein links
DNA binding protein PDB id
2aje
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8L7L8  (TRP1_ARATH) -  Telomere repeat-binding protein 1
Seq:
Struc:
 
Seq:
Struc:
578 a.a.
97 a.a.
Key:    PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chromatin binding     2 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18583523 A.Guerler, and E.W.Knapp (2008).
Novel protein folds and their nonsequential structural analogs.
  Protein Sci, 17, 1374-1382.  
  20664721 E.V.Shakirov, S.L.Salzberg, M.Alam, and D.E.Shippen (2008).
Analysis of Carica papaya Telomeres and Telomere-Associated Proteins: Insights into the Evolution of Telomere Maintenance in Brassicales.
  Trop Plant Biol, 1, 202-215.  
  18684336 P.Agudelo-Romero, P.Carbonell, F.de la Iglesia, J.Carrera, G.Rodrigo, A.Jaramillo, M.A.Pérez-Amador, and S.F.Elena (2008).
Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus.
  Virol J, 5, 92.  
18367475 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, and H.S.Cho (2008).
Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins.
  Nucleic Acids Res, 36, 2739-2755.
PDB code: 2ckx
17272298 M.G.Hwang, and M.H.Cho (2007).
Arabidopsis thaliana telomeric DNA-binding protein 1 is required for telomere length homeostasis and its Myb-extension domain stabilizes plant telomeric DNA binding.
  Nucleic Acids Res, 35, 1333-1342.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.