Different mechanisms for translocation by monomeric and hexameric helicases

Abstract

Helicases are ATP-dependent motor proteins that translocate along single-stranded or double-stranded nucleic acids to alter base-pairing structures or molecular interactions. Helicases can be divided to monomeric and hexameric types, each with distinct ternary structures, nucleic acid-binding modes, and translocation mechanisms. It is well established that monomeric helicases translocate by the inchworm mechanism. Recent structures of different superfamilies of hexameric helicases reveal that they use a hand-over hand mechanism for translocation. Structures of bacteriophage T7 replisome illustrate how helicase and polymerase cooperatively catalyze DNA unwinding. In this review, we survey structures of monomeric and hexameric helicases and compare different mechanisms for translocation.

Figure 1.

Structure and mechanism of monomeric helicases. (a-b) Cut-open views of SF1 UvrD-DNA complexes without (a) or with ATP (b). DNA interaction residues are highlighted in stick representation and the separation pin is indicated by a black arrow. The alternative tight and loose interactions are indicated by the hand icons in the schemes below each panel. (c) Structure of SF1 RecD2 complexed with ssDNA and ATP analog. The tight and loose interactions are indicated and are reverse of that in UvrD. (d) Structures of HCV NS3 (SF2 RNA helicase) with ssDNA and ATP analog. (e) Structure of Snf2 (SF2) complexed with nucleosome and ATP analog. The RecA domains of HCV NS3 are overlaid (transparent light green and blue), and ssDNA bound to HCV NS3 is shown in magenta. In all panels, domains 1A and 2A are colored green and blue, respectively, and inserted domains are shown in light orange. The ATP (or its analogs) and Mg²⁺ are depicted as sticks and balls. The tracking DNA strand bound to UvrD, RecD2, HCV NS3, and Snf2 are colored orange, pink, ruby and cyan, respectively. The directions of helicase translocation are marked by grey arrows in panel a-e. (f) Superpositions of ssDNA or dsDNA substrates bound to SF1 and SF2 helicases. (g) Diagram of ATPase dependent inchworm movement of helicase translocation.

Figure 2.

Structure of hexameric helicases. (a-f) Orthogonal views of hexameric helicase-DNA complexes of gp4 (a-b), E1 (c-d), and CMG (e-f). The N-terminal domains (NTD, or primase (Pri) domain in gp4) are shown as semi-transparent molecular surfaces, and the C-terminal helicase (Hel) domains are shown in cartoons. The subunits in gp4 and E1 are marked as A-F following the order from the 3′-to-5′ end of the DNA and colored in blue, light magenta, green, cyan, yellow, and red, respectively. The MCM subunits in CMG complexes followed the same color scheme while the MCM4 and MCM7 are in light blue and red to indicate that they are not involved in DNA binding. HelF subunits in gp4 and E1 as well as MCM4 and MCM7 in CMG are omitted in panels a, c, e, for clarity. The translocated position of HelF in gp4 are indicated by red outline or oval. The directions of helicase translocation are marked by grey arrows in panel a, c, e. (g) Superposition of DNAs in these helicase complexes with B-DNA (black and grey). (h) The hand-over-hand translocation mechanism of hexameric helicase base on gp4 helicase structures.

Figure 3.

Helicases in bacterial and yeast replisomes. (a) Structure of the T7 replisome. The “T” shaped DNA fork is highlighted by an overlaid semi-transparent T. (b) A zoom-in view of the T7 replication fork. A β hairpin in the leading-strand DNA polymerase is at the fork to promote DNA strand separation. (c) The cryoEM image of yeast CMG, Pol ε and Pol α (primosome) assembled on a DNA fork reveals a three-tier-core structure [14], similar to that of the phage T7 replisome shown in (a). (d) Diagrams of the DNA fork substrate in the three-tier-core replisome from bacteria and eukaryotic systems. The conserved DNA part are shown in orange, and the different downstream parental DNA in bacterial and eukaryotic replisome are shown in pink and yellow, respectively.