Structure of UvrA nucleotide excision repair protein in complex with modified DNA

Abstract

One of the primary pathways for removal of DNA damage is nucleotide excision repair (NER). In bacteria, the UvrA protein is the component of NER that locates the lesion. A notable feature of NER is its ability to act on many DNA modifications that vary in chemical structure. So far, the mechanism underlying this broad specificity has been unclear. Here, we report the first crystal structure of a UvrA protein in complex with a chemically modified oligonucleotide. The structure shows that the UvrA dimer does not contact the site of lesion directly, but rather binds the DNA regions on both sides of the modification. The DNA region harboring the modification is deformed, with the double helix bent and unwound. UvrA uses damage-induced deformations of the DNA and a less rigid structure of the modified double helix for indirect readout of the lesion.

Surviving the Sun: Repair and bypass of DNA UV lesions

“…Only DDB2 of XPE, which specifically enhances recognition of UV lesions in GG-NER, interacts directly with a UV lesion. 36 UvrA, UvrB, and XPC make no direct contact with DNA lesions, 28,34,35 which is consistent with the fact that they have no special preference for a particular lesion type. The lesions are disordered in cocrystal structures with UvrA, UvrB, and XPC-HR23B.…”

“…23,24 Molecular mechanisms for coping with UV lesions by different repair pathways and translesion DNA synthesis have been extensively studied. In the last few years the structures of UvrA, UvrB, XPC, and XPE, which carry out the first step of UV-lesion recognition in bacteria and eukaryotes, have been determined alone or complexed with DNA substrates, [25][26][27][28][29][30][31][32][33][34][35][36] as have yeast and human DNA pol g complexed with CPDs. 37,38 DNA base lesions, which include mismatched basepairs, modified bases due to oxidation, deamination, or alkylation, losses of bases (abasic sites) and large base adducts like cisplatin and polyaromatic hydrocarbons, exhibit a general feature of reduced base stacking and reduced DNA persistence length (see the review 39 and references therein).…”

“…10,18 Consistent with their lesion recognition roles, XPC and DDB2 are not required in TCR. 12 In the UvrA-DNA complex (without an ATP or ADP analog) structure, which contains two fluorescein labeled thymines as mimics of damaged bases, the DNA appears to be fully base paired and nearly straight 34 [ Fig. 4(B)].…”

The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action

“…In contrast, when we modelled the modified DNA molecule as observed in Tm UvrA•DNA structure (17) in the optimally superimposed Mt UvrA dimer, steric hindrance became appreciable on both sides of the fluoresceinated-dT containing lesion at the level of both the UvrB-BD and the C-terminal Zn fingers (Figure 6b and Supplementary Movie).

Figure 6.Modelling of double-strand DNA binding within the Mt UvrA dimer.

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“…The resulting Mt UvrA•UvrB complex would be compatible with both an UvrA 2 •UvrB 2 (Figure 7b, upper panels) and an UvrA 2 •UvrB (not shown) stoichiometry. Moreover, the different conformation adopted by the UvrB-BD, respectively, in the structure of ligand-free Mt UvrA, Bst UvrA•ADP (16) and Tm UvrA•DNA (17) (Figure 7b, from top to bottom), appears in all cases competent for the concomitant association to UvrB and DNA, although with different geometry. In fact, while in the Mt UvrA 2 •UvrB 2 model the double-strand DNA should be hosted inside an only partially solvent-accessible track, which is built up by the facing ventral surfaces of both protein components, in the other two models the UvrB-BD repositioning would result in the exposure of the DNA molecule to the bulk solvent.…”