DNA Helicases- Definition, Structure, Types, Functions, Examples

DNA helicases are ubiquitous enzymes found in all domains of life and associated with nucleic acid metabolisms such as DNA replication, transcription, translation, DNA repairing, recombination, ribosome biogenesis, and decay.

DNA helicase was discovered first in E. coli in 1976.

They are ATP (adenosine triphosphate) dependent separating enzymes that promote separation of the two parental strands and unwind DNA at a position called the origin of replication from where replication starts. It formed a replication fork that will progressively move away from its origin due to the continued unwinding of DNA.

Unwinding of the template DNA helix at a replication fork principally catalyzed by two DNA helicases, acting in concert, one running along the leading strand and the other the lagging strand.

DNA helicases
DNA helicase.

Helicases use ATP as a source of energy to break the hydrogen bond between the nitrogenous base pairs of double standard DNA. 

In addition, some DNA helicases also unwind DNA triplexes or G-quadruplexes and displace protein bound to single or double-standard DNA. 

All helicases share at least three common biochemical properties:

1) nucleic acid binding

2) NTP/dNTP binding and hydrolysis

3) NTP/dNTP hydrolysis-dependent unwinding of duplex nucleic acids in the 3’ to 5’ or 5’ to 3’ direction.

 Structure of DNA helicases

  • Two different types of helicases structure exist, those rings forming hexameric structures and those that do not.
  • A ring structure has a central channel that encircles the nucleic acid. The stability and processivity of the enzyme increase with increasing topological links between the protein and the nucleic acid.
  • All hexameric helicases are homohexamers except the eukaryotic minichrosomal maintenance helicases. 
  • Helicase motifs mean nine short conserved amino acid sequence finger-prints (designated Q, I, la, lb, II, III, IV, V, and VI) contained in most of the helicases from different organisms.
  • These motifs are generally clustered in the central region i.e. region of 200 to 700 amino acids.  

Types of DNA helicases

  • Multiple DNA helicases have been isolated from single-cell because of the different structural requirements of the substrate at various stages in the DNA transaction. For example, a Minimum of 14 DNA helicases were isolated from E. coli, 12 from viruses, 6 from bacteriophages, 8 from plants, 15 from yeast, 11 from the thymus of the calf, and about 24 from a human cell.
  • Helicases can be divided into 6 superfamilies (SF1 TO SF6) based on identified sequences among conserved helicase motifs.
  • The toroidal enzyme, ring forming, a hexameric structure consists of SF3 to SF6 and the ring not forming ones consists of SF1 and SF2. Those ring-like structure permits the encircling of the DNA and translocates in a processive fashion.

Superfamily SF1:

  • The several structures of SF1 helicases have a common core with two α-β RecA-like domains. They are monomerically involved in recombination, transcription, repair, and other processes.
  • The structural homology with RecA recombination protein enfolds the tandem alpha-helices and the five contiguous parallel beta-strands. 
  • ATP binds at the amino proximal α-β domain that contains motif I (walker A) and motif II (walker B). Motif III (S-A-T) is also present in the N-terminal domain that will help to the established link between the activities of ATPase and helicases. The carboxy-terminal α-β domain is structurally similar to the proximal domain although it lacks an ATP-binding site which may be originated from gene duplication.
  • Superfamily SF1 is further divided into three subfamilies (PiF1/RecD, Rep/UrvD, and UpF1 like) and two groups 3’to 5’ for SF1A and 5’ to 3’for SF1B on the basis of translocation direction on SSDNA.
DNA helicase Superfamily SF1
Figure: Crystal structures of SF1A (PcrA, UvrD) and SF1B (RecD2, Dda) helicases. Image Source: Kevin D. Raney et al. 2013.

Superfamily SF2:

  • They play important role in RNA metabolism, and various steps in DNA metabolism.
  • Within superfamily 2 they are 10 separate families of helicases are found. Each plays a specific role in nucleic acid metabolism.

Superfamily SF3:

  •  Helicases predominantly encoded by small DNA and RNA viruses and large nucleocytoplasmic DNA viruses are falls under this category.
  • In SF3 helicases the spacer separates walker A motifs and Walker B motifs. Third motif C resides between the B motif and the C-terminus of the conserved region.

Superfamily SF4: 

  • It is a hexameric helicase that functions mainly in bacterial (related to bacterial dnaB protein) or bacteriophage replication.
  • The central core is similar to the α-β RecA- like domain.

Superfamily SF5:

  • The E. coli Rho factor is an SF5 hexamer that terminates particular RNA transcripts, translocates only on RNA, and sheds ample light on replicative helicases function.

Superfamily SF6:

  • They include the AAA+ core which is not present in SF3. Some proteins of this group are minichromosome maintenance (MCM) like RuvA, RuvB, and RuvC.

Mechanism of DNA helicases

Mechanism of DNA helicases
Figure: Proposed Brownian ratchet mechanism and most likely kinetic scheme. Image Source: Daniel R. Burnham et al. 2019.
  • DNA helicases are essential motor proteins that function to unwind duplex DNA to yield the transient single-stranded DNA intermediates required for replication, recombination, and repair.
  • Although helicase describes a similar three-dimensional fold, various oligomeric states are assembled to display full activity.  hexameric assembly is the most established among others in which six subunits of helicases assemble to form such ring-shaped hexameric class of helicases.
  • In a double helix, oligomerization of the subunit is stabilized by binding NTP or metal ions.
  • Out of 6 potential ATP binding sites, two opposite binds ATP tightly, two bind ADP and pi and two subunits are empty.
  • The proximity between ATP and ATP binding site is most crucial for forming a covalent bond between enzyme and sugar-phosphate backbone of DNA and this energy from hydrolysis of ATP helps to overcome the activation barrier.
  • When ATP is hydrolyzed these 3 states interconvert in a coordinating fashion forming a ripple effect.
  • The continuous ripple effect that runs around the ring causes some conformational changes and the loop extends into the center of the hole of a ring that (binds DNA).
  • This ups and down oscillating loop drag a DNA strand from the center of the hole leading to the separation of the DNA double helix into a single strand.

Functions of DNA helicases

  1. DNA helicases unwind or separate the hydrogen bonds between nucleotides bases of two strands of double-stranded DNA by the use of the energy equivalent ATP.
  2. DNA helicases play mandatory roles in homologous somatic genome stability and meiotic mixing of the parental genomes in plants. 
  3. The FANCJ is the DNA helicase mutated in ovarian cancer, hereditary breast, and progressive bone marrow failure disorder (Fanconi anemia) that disturbs helicase activity. This FANCJ helps in cancer suppression and directly interacts with BRCA1 for double-strand break repair.
  4. Some helicases (for example, RECQL1, RECQL4, RECQL5, WRN, and BLM) carry out strand annealing by promoting base pairing.
  5.  They play an active role in the transmission of genetic information from one generation to the next.

Examples of DNA helicases

E. coli DNA helicases:

  • DnaB: It is a replicative helicase, that works on a replication fork basically on a lagging strand.
  • Helicase II(UvrD): It is involved in nucleotide excision repair.

Bacteriophages DNA helicases:

  • T4 UvsW: Catalyzes branch migration and plays a mandatory role in DNA recombination, regulation of origin of replication, and DNA repair.

Viral DNA helicases:

  • HSV-1, UL9 protein:  origin binding protein involved during the initiation of HSV replication.

Yeast DNA helicases:

  • PIF1: Functions in mitochondrial DNA repair and recombination.

Human DNA helicases:

  • HDH VI: Prefers structure of substrates just like replication fork.

References

  1. Burnham, D.R., Kose, H.B., Hoyle, R.B. et al. The mechanism of DNA unwinding by the eukaryotic replicative helicase. Nat Commun 10, 2159 (2019). https://doi.org/10.1038/s41467-019-09896-2
  2. Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol. 2013;767:17-46. doi:10.1007/978-1-4614-5037-5_2
  3. Uchiumi, F., Seki, M., Furuichi, Y., eds. (2015). DNA Helicases: Expression, Functions and Clinical Implications. Lausanne: Frontiers Media. doi: 10.3389/978-2-88919-575-6
  4. Alexander Knoll, Holger Puchta, The role of DNA helicases and their interaction partners in genome stability and meiotic recombination in plants, Journal of Experimental Botany, Volume 62, Issue 5, March 2011, Pages 1565–1579, https://doi.org/10.1093/jxb/erq357
  5. Patel SS, Donmez I. Mechanisms of helicases. J Biol Chem. 2006 Jul 7;281(27):18265-8. doi: 10.1074/jbc.R600008200. Epub 2006 May 2. PMID: 16670085.
  6. Lewin B (2007), Genes IX, Oxford University Press, and Cell Press.
  7. Verma, P. S., & Agrawal, V. K. (2006). Cell Biology, Genetics, Molecular Biology, Evolution & Ecology (1 ed.). S . Chand and company Ltd.
  8. Tuteja, N., & Tuteja, R. (2004). Unraveling DNA helicases: motif, structure, mechanism, and function. European Journal of Biochemistry271(10), 1849-1863.
  9. Tuteja, N., & Tuteja, R. (2004). Prokaryotic and eukaryotic DNA helicases: essential molecular motor proteins for cellular machinery. European Journal of Biochemistry271(10), 1835-1848.
  10. Fairman-Williams, M. E., Guenther, U. P., & Jankowsky, E. (2010). SF1 and SF2 helicases: family matters. Current opinion in structural biology20(3), 313-324.
  11. https://www.ebi.ac.uk/interpro/entry/InterPro/IPR014001/
  12. https://prosite.expasy.org/PDOC51206

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