PDBsum entry 1ign

DNA binding protein/DNA

PDB id

1ign

Contents

			Protein chains

					189 a.a. *

			DNA/RNA

			Waters ×206

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The crystal structure of the DNA-Binding domain of yeast rap1 in complex with telomeric DNA.

Authors

P.Konig, R.Giraldo, L.Chapman, D.Rhodes.

Ref.

Cell, 1996, 85, 125-136. [DOI no: 10.1016/S0092-8674(00)81088-0]

PubMed id

8620531

Abstract

Telomeres, the nucleoprotein complexes at the ends of eukaryotic chromosomes, are essential for chromosome stability. In the yeast S. cerevisiae, telomeric DNA is bound in a sequence-specific manner by RAP1, a multifunctional protein also involved in transcriptional regulation. Here we report the crystal structure of the DNA-binding domain of RAP1 in complex with telomeric DNA site at 2.25 A resolution. The protein contains two similar domains that bind DNA in a tandem orientation, recognizing a tandemly repeated DNA sequence. The domains are structurally related to the homeodomain and the proto-oncogene Myb, but show novel features in their DNA-binding mode. A structured linker between the domains and a long C-terminal tail contribute to the binding specificity. This structure provides insight into the recognition of the conserved telomeric DNA sequences by a protein.



	Figure 4. Figure 4. Summary of Protein–DNA ContactsThe DNA is represented as an opened-out helix. Direct hydrogen bonds between the protein and the DNA are indicated by arrows. Water (W)-mediated interactions are shown by broken arrows. Hydrophobic contacts are indicated by arrows with round heads (Me, methyl group of thymidine; C, C5 atom of cytosine). Contacted phosphate groups (black) and deoxyribose rings (gray) are indicated by closed circles.		Figure 6. Figure 6. Comparison of the Structure of the RAP1 DBD with the Engrailed Homeodomain and Myb(a) Superposition of domain 1 (pale green) with domain 2 (orange) of RAP1 in a view along the recognition helices. The structures were overlaid using the protein alone. The corresponding DNA sites are shown in blue for domain 1 and cyan for domain 2. The C-terminal region of domain 1 is omitted for clarity.(b) Superposition of the Engrailed homeodomain (white) with domain 1 of RAP1 (pale green). The structural similarity includes the three-helix bundle and the N-terminal arm (domain 1 of RAP1, residues 360–378, 387–396, and 398–409; Engrailed, residues 5–23, 30–39, and 40–51, numbered according to pdb entry 1hdd). The DNA sites (RAP1, blue; Engrailed, white) are shown to illustrate the different docking of the domains on DNA.(c) Superposition of the second repeat of the proto-oncogene Myb (magenta) with domain 1 of RAP1 (pale green). The structural similarity extends over the three-helix bundles (domain 1 of RAP1, residues 363–378 and 387–409; Myb, residues 94–100 and 114–136, numbered according to pdb, entry 1 mse). The view is rotated by 90° about the DNA axis with respect to (a) and (b) to illustrate the different position of the recognition helices in the major groove of their DNA sites (RAP1, blue; Myb, magenta).