PDBsum entry 2qsg

DNA binding protein/DNA

PDB id: 2qsg

Contents

Protein chains

502 a.a.

54 a.a.

DNA/RNA

References listed in PDB file

Key reference

Title

Recognition of DNA damage by the rad4 nucleotide excision repair protein.

Authors

J.H.Min, N.P.Pavletich.

Ref.

Nature, 2007, 449, 570-575. [DOI no: 10.1038/nature06155]

PubMed id

17882165

Abstract

Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson-Crick double helix in a manner that facilitates the flipping-out of two base pairs.

Figure 3.
Figure 3: Rad4 binds to damaged DNA in two parts. a, TGD–BHD1 binds to an 11-bp segment of undamaged dsDNA, making extensive contacts to the DNA phosphate and ribose groups. Close-up view of the TGD–DNA interface, in an orientation similar to Fig. 1a, showing side-chain and backbone groups that contact the DNA. Green dotted lines indicate hydrogen bonds. b, Close-up view of the BHD1–dsDNA interface, in an orientation slightly rotated about the DNA axis relative to a. c, Schematic representation of the interactions shown in a and b. Van der Waals contacts to DNA, orange arrows; polar contacts between side chains and DNA, green arrows; and hydrogen bonds between backbone amide and DNA phosphate groups, blue arrows. d, BHD2–BHD3 bind to a 4-bp DNA segment that contains the CPD lesion. Close-up view of the interface in a similar orientation as in Fig. 1a, showing side chains that contact the DNA. The flipped-out thymidines of the undamaged strand are coloured black, and the disordered, CPD-linked thymidines are indicated schematically. e, Schematic representation of the interactions shown in d. Contacts are marked with arrows, as described in c.

Figure 4.
Figure 4: Rad4 undergoes conformational changes on DNA-binding. a, The Rad4–Rad23–DNA complex (red) is superimposed on the apo-Rad4–Rad23 complex (green) by aligning the TGDs. Black arrows indicate the movement of BHD1, BHD2 and BHD3 towards the DNA in the DNA-bound structure relative to the apo-Rad4–Rad23 structure. The BHD3 tip in the apo-Rad4–Rad23 structure is disordered and is not shown. The Rad23 R4BD is omitted for clarity. b, Model of undamaged B-type dsDNA bound to Rad4 showing that the apo-Rad4 but not the DNA-bound Rad4 conformation would allow binding to undamaged dsDNA. The model was prepared by superimposing a B-type dsDNA on the undamaged dsDNA portion of the Rad4–Rad23–DNA structure.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 570-575) copyright 2007.