PDBsum entry 2ja7

Transferase

PDB id: 2ja7

Contents

Protein chains

1421 a.a.

1115 a.a.

267 a.a.

177 a.a.

214 a.a.

87 a.a.

171 a.a.

135 a.a.

116 a.a.

65 a.a.

114 a.a.

46 a.a.

DNA/RNA

Metals

_ZN ×16

_MG ×2

References listed in PDB file

Key reference

Title

Cpd damage recognition by transcribing RNA polymerase ii.

Authors

F.Brueckner, U.Hennecke, T.Carell, P.Cramer.

Ref.

Science, 2007, 315, 859-862. [DOI no: 10.1126/science.1135400]

PubMed id

17290000

Abstract

Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.

Figure 1.
Fig. 1. Pol II elongation complex structures with thymine-thymine CPD lesions in the template. (A) Nucleic acid scaffolds A to D. The color code is used throughout. Filled circles denote nucleotides with interpretable electron density that were included in the structures in (B). Open circles denote nucleotides having electron density that could not be interpreted or that was lacking. (B) Structure of nucleic acids in the Pol II elongation complexes A to D. The view is from the side (11). Figures prepared with PYMOL (DeLano Scientific). (C) Overview of complex C with a CPD lesion at the active site. The view is as in (B). Protein is in gray, the bridge helix in green. The CPD is shown as a stick model in orange. A large portion of the second largest Pol II subunit was omitted for clarity. (D) Superposition of nucleic acids in structures A to D. The protein molecules were superimposed and then omitted. The nucleic acids are depicted as ribbon models, the CPDs as stick models. Upper and lower views are related by a 90° rotation around a horizontal axis.

Figure 3.
Fig. 3. Mechanism of CPD recognition by transcribing Pol II. Schematic representation of RNA extension in complex A. The initial RNA (top) corresponds to the nonextended RNA of scaffold A. The translocation barrier and the translocation block are indicated with a dashed and a solid horizontal line, respectively. The artificial situation leading to lesion bypass (Fig. 2E) is depicted at the bottom.

The above figures are reprinted by permission from the AAAs: Science (2007, 315, 859-862) copyright 2007.