Crystal structure of Deinococcus radiodurans RecQ helicase catalytic core domain: the interdomain flexibility

Abstract

RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ from Deinococcus radiodurans (DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of the E. coli RecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

Figure 1

(a) Crystal structure of the D. radiodurans RecQ catalytic core. The two RecA-like domains, D1 and D2, are colored in blue and red, respectively. The zinc-binding domain is highlighted in orange and the WH domain in green. ADP (magenta) is depicted in stick representation. (b) The size exclusion chromatography profile of DrRecQ. (c) The zinc-binding site of DrRecQ. The four conserved cysteine residues are shown in stick and a zinc ion is colored in magenta. The 2F_o-F_c electron density map contoured at the 2σ level is colored in gray.

Figure 2

(a) The electron density for ADP from F_o-F_c map seen at 3σ. (b) Stereo view of the catalytic site in the DrRecQ catalytic core. The residues that interact with ADP in DrRecQ are shown as ball-and-stick models (magenta). Main chain and carbon are colored according to the conserved motifs: motif 0 (cyan) and motif I (green).

Figure 3

Sequence alignment of the catalytic core from various RecQ proteins. Conserved helicase motifs 0 and I are labeled and enclosed in blue boxes. The conserved residues are shaded in red.

Figure 4

(a) Overlay of DrRecQ (magenta) and EcRecQ (blue). Structures were superposed using the RecA-like 2 domain as a reference. (b) Structure comparison of β-hairpins between RecQ members. The DrRecQ (magenta) is shown overlaid with human RecQ1 (yellow) and with E. coli RecQ (blue).

Figure 5

Interdomain flexibility of DrRecQ. The apoform is colored in magenta and the ADP-bound form in green. The structures are superimposed by using the RecA-like 2 domain as a reference.