Helicases: what are Definition, Structure and Function?

What is helicase?

Helicase are ubiquitous enzymes found in all organisms. It s involved in all aspects of nucleic acid or  nucleic acid protein complexes metabolism. There are DNA and RNA helicases. DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied.

The role of the helicases is to utilize the energy derived from nucleoside triphosphate hydrolysis to translocate along nucleic acid strands, unwind/separate the helical structure of double-stranded nucleic acid, and, in some cases, disrupt protein–nucleic acid interactions. Because of their essential function, helicases are ubiquitous and evolutionary conserved proteins.

What is the Structure and Activities of Helicase?

Helicases are characterized by the presence of conserved motifs in the form of short amino acid sequences. Based on variations of the number of motifs, their amino acid sequence, and spacing, helicases are grouped into superfamilies,

This include three large (SF1–SF3) and two small (SF4 and SF5) ones. SF1 and SF2 have at least seven conserved motifs (I, Ia, II, III, IV, V, and VI) and are monomers, whereas SF3–SF5 members assemble into hexamers.

The crystal structures of several representative helicases were resolved and revealed common features. Monomeric helicases have a core that consists of two domains with a linker region. Hexameric helicases form a core that includes six individual domains arranged in a ring. The domains are termed RecA-like because of the similarity to the ATP-binding core of RecA recombination protein.

The conserved helicase motifs include those involved in ATP binding and hydrolysis, which are similar to the Walker A and B boxes of ATPase. The other conserved motifs are involved in coupling of the ATP hydrolytic state to protein conformational changes and in nucleic acid binding.

Helicase core structure allows for cycles of nucleic acid binding and release driven by ATP binding and hydrolysis . By utilizing the energy derived from ATP hydrolysis, helicases function as nucleic acid motor or translocases.

Helicase activities are described in terms of rate, processivity, directionality, and step size. Rate is the number of unwound/ translocated base pairs, or the number of ATP molecules hydrolyzed, per unit time.

Processivity is the number of base pairs unwound/translocated before the helicase dissociates from the nucleic acid. Directionality is the bias exhibited by a processive helicase in its movement along nucleic acids, either 3׳ to 5׳ or 5׳ to 3׳ direction.

Finally, step size has been described as either mechanical (the average distance moved) or kinetic (the average number of unwound/ translocated) during each catalytic cycle.

Depending on the type of their nucleic acid targets, helicases are generally classified as DNA or RNA helicases. Some helicases can unwind both targets, whereas others preferentially unwind RNA–DNA duplexes.

DNA helicases are involved in replication, repair and recombination. RNA helicases are involved in all aspects of RNA metabolism.

Mechanism of Action

The catalytic activity of DNA helicase starts with recognizing the dsDNA strand. Interestingly, DNA helicase required a short stretch of the ssDNA for performing the unwinding during in vitro experiments. 

Nonetheless, how the helicase starts unwinding the dsDNA, in vivo (during replication) is still not known.  In simple words, we can say that the helicase is a kind of rotating engine that moves forward to perform its activity. 

Helicase moves forward at the rate of one nucleotide per hydrolysis reaction. The activity of the helicases varies from enzyme to enzyme, some are bidirectional (works on both sides) while some are unidirectional (works on a single side). 

For instance, the ReBCD helicase performs the catalytic activity in both directions, 5’ to 3’ and 3’ to 5’ while the RecB helicase performs the enzymatic reaction unidirectionally, only from 3’ to 5’. 

Different motif present in the core of the enzyme helps in processing the ATP.  The ATP converts into ADP and releases the energy which is utilized to activate the jet engine of helicase. 

The human hexameric helicase has a central holo part in which the DNA binding motif is present. Once the DNA entred into the holo part, the motifs Walker A and Walker B start hydrolysis of ATP and release energy to break the hydrogen bond.

Once it starts spinning, it breaks the hydrogen bonds and moves forward, again, for another set of reactions, it utilizes another ATP. During this process, the helicase binds to one of the two dsDNA strands and passes it from its hollow core.

what is the Function of Helicase Enzyme?

Unwinding the double-stranded nucleic acid (DNA/RNA) is a major function of any helicase subclass enzyme.  In DNA replication, the helicase works by creating a complex with other proteins such as DNA primase, polymerase, or single stranded-binding proteins. 

During replication, the helicase unwinds the dsDNA as we discussed above. Apart from this, several other functions are also performed by the helicase which is enlisted below, During DNA repair, the helicase unwinds or opens the dsDNA for repairing damaged DNA strands. 

During the translation, it breaks the hydrogen bonds between the DNA-RNA hybrid. Further to this, the helicase also helps in splicing, chromatin remodeling, termination of translation. 

Functions performed by the RNA helicase in RNA biogenesis are: 

  • RNA editing, 
  • RNA unwinding
  • RNA degradation
  • RNA splicing
  • RNA transport 

It also facilitates the metabolism of nucleic acids by facilitating the ssNA (single-stranded nucleic acid). Furthermore, the helicase provides the strand migration or exchange of genetic material during the process of recombination.

Interestingly, scientists have found that helicase is also involved in the telomerase maintenance and aging process. 

Several helicases and their function are given into the table below, 

Helicases Function 
PcrA1, RepA, Dna2, NS3, RecD, TraI, HSv UL9, Dna BInvolved in DNA replication 
Dna2, WRN, Pif1Involved in Okazaki fragment maturation at the lagging strand 
Factor 2, Rho, SWI2, SNF2, TFIIHInvolved in transcription 
Rtel1, BLM, Rho, PriA, UvrD, RecQ, RecG, RecBCD, Tra IInvolved in recombination 
RuvB, Mph 1, RecQ, WRN, Helicase E, UvrD, RecD2 and RecQInvolved in DNA repair mechanism 
Vasa, HSV UL5, RHA and eIF4A Translation 
BLM, Rtel 1, Pif1, Dna2 Telomere maintenance 
BLM, ATRX, Rad54 Chromatid remodelling

Several helicases play an important role in the DNA translation too are: 

TFIIH- activation of translation 

TFIIH, SNF1- initiation of translation 

SW1, TFIIH, SW1, Rho and Factor 2 for maintenance, DNA repair and translation termination. 

Apart from its role in DNA maintenance, the mutation in the helicase coding gene also results in some genetic anomalies.  ATRX helicase mutation, XPD point mutation, and RecQ mutations are some of the common mutations found in the helicase. 

Various mutations in the helicase enzyme coding genes result in abnormal conditions like immunodeficiency, mental retardation, premature aging, and cancer.  Some of the diseases in which the helicase is involved are Bloom’s syndrome, alpha-thalassemia, xeroderma pigmentation, and Cockayne syndrome.