PDBsum entry 1w0t

DNA binding protein

PDB id: 1w0t

Contents

Protein chains

52 a.a.

DNA/RNA

Waters ×72

References listed in PDB file

Key reference

Title

How the human telomeric proteins trf1 and trf2 recognize telomeric DNA: a view from high-Resolution crystal structures.

Authors

R.Court, L.Chapman, L.Fairall, D.Rhodes.

Ref.

EMBO Rep, 2005, 6, 39-45. [DOI no: 10.1038/sj.embor.7400314]

PubMed id

15608617

Abstract

Human telomeres consist of tandem arrays of TTAGGG sequence repeats that are specifically bound by two proteins, TRF1 and TRF2. They bind to DNA as preformed homodimers and have the same architecture in which the DNA-binding domains (Dbds) form independent structural units. Despite these similarities, TRF1 and TRF2 have different functions at telomeres. The X-ray crystal structures of both TRF1- and TRF2-Dbds in complex with telomeric DNA (2.0 and 1.8 angstroms resolution, respectively) show that they recognize the same TAGGGTT binding site by means of homeodomains, as does the yeast telomeric protein Rap1p. Two of the three G-C base pairs that characterize telomeric repeats are recognized specifically and an unusually large number of water molecules mediate protein-DNA interactions. The binding of the TRF2-Dbd to the DNA double helix shows no distortions that would account for the promotion of t-loops in which TRF2 has been implicated.

Figure 3.
Figure 3 Summary of direct protein -DNA contacts in the TRF1-Dbd -DNA and TRF2-Dbd -DNA complexes. (A) Maps of protein -DNA contacts. The DNA is represented as an opened-out helix. Red lines indicate direct hydrogen bonds. These contacts are conserved between the two molecules in one complex. Direct contacts in the minor groove made by residues R380 of TRF1 and K447 of TRF2 that differ in the two protein molecules in one complex are indicated by dotted and dashed red lines. A dashed blue line depicts water-mediated contacts. (B) Views at atomic resolution of the hydrogen bonds between residues in the DNA-recognition helix and the bases in the major groove of DNA.

Figure 4.
Figure 4 Summary of water-mediated protein -DNA contacts in the TRF1-Dbd -DNA and TRF2-Dbd -DNA complexes. (A) Conservation in the water structure at the protein -DNA interface. The two proteins are shown as ribbon representations and only half of each complex is shown. Conserved water molecules at the protein -DNA interface are represented by blue spheres. (B) Summary of water-mediated contacts in TRF1-Dbd -DNA and TRF2-Dbd -DNA complexes. Conserved water molecules are shown in blue and additional water molecules are shown in yellow. Blue dashed lines depict the network of water-mediated hydrogen bonds.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO Rep (2005, 6, 39-45) copyright 2005.