Superfamily 2 helicases

Abstract

Superfamily 2 helicases are involved in all aspects of RNA metabolism, and many steps in DNA metabolism. This review focuses on the basic mechanistic, structural and biological properties of each of the families of helicases within superfamily 2. There are ten separate families of helicases within superfamily 2, each playing specific roles in nucleic acid metabolism. The mechanisms of action are diverse, as well as the effect on the nucleic acid. Some families translocate on single-stranded nucleic acid and unwind duplexes, some unwind double-stranded nucleic acids without translocation, and some translocate on double-stranded or single-stranded nucleic acids without unwinding.

Figure 1

Structure of DEAD-box helicase Mss116p. A. The crystal structure (Protein Data Bank code 3I61 (41)) of the DEAD-box helicase Mss116p bound to ssRNA and the ATP transition state analog, ADP-BeF₃⁻, illustrates the bending of the nucleic acid substrate by DEAD-box helicases. The helicase motifs are in the cleft formed between the two RecA-like domains. B. The consensus sequence for the conserved helicase motifs (1, 34) in DEAD-box family members is shown.

Figure 2

Proposed destabilization mechanism for unwinding by DEAD-box helicases (34, 37). The helicase (yellow oval) binds to the ATP (green triangle) and dsRNA (black lines) (step 1). Following a rearrangement (step 2) one strand of RNA can dissociate (step 3). ATP hydrolysis occurs after unwinding (step 4), and the cycle is completed with the release of phosphate (red triangle), ssRNA, and ADP (blue trapezoid) (step 5).

Figure 3

The crystal structure of the human RecQ1 (Protein Data Bank code 2WWY (23)) shows the beta-hairpin separating the strands of duplex DNA. The two RecA-like domains are colored in green and gray. The Zn domain is purple. The winged helix domain is cyan, and the beta-hairpin is red.

Figure 4

A. Families containing helicases that unwind duplex nucleic acids using a mechanism dependent on translocation upon the substrate contain a beta-hairpin. The Protein Data Bank codes are RecQ1: 2WWY (23), NS3: 1A1V (63), Hel308: 2P6R (85), and Prp43p: 2XAU (74). B. XPD (Protein Data Bank code 2VSF (100)) has translocase and helicase activity, but does not have a beta-hairpin. Instead, the wedge appears to be formed from two alpha-helices (100). RecG (Protein Data Bank code 1GM5 (162)) has a beta-hairpin and a wedge domain which simultaneously separate two arms of a DNA fork. C. Families which either do not unwind nucleic acids, or unwind without translocating, do not have the beta-hairpin. The Protein Data Bank codes are Mss116p: 3I61 (41), SWI2/SNF2: 1Z63 (166), Hef: 1WP9 (167), and EcoR124I: 2W00 (168). In each of the structures, the N-terminal RecA-like domain is navy and the C-terminal RecA-like domain is green. Accessory domains are gray, except the beta-hairpin, which is red and wedge domains are purple. Nucleic acid is yellow and nucleotide is green.