Helicase

Helicase

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Helicases are a class of enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

s vital to all living organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

s. They are motor proteins that move directionally along a nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...

 phosphodiester backbone
Phosphodiester bond
A phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates over two ester bonds. Phosphodiester bonds are central to all known life, as they make up the backbone of each helical strand of DNA...

, separating two annealed nucleic acid strands (i.e., DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

, RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

, or RNA-DNA hybrid) using energy derived from ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

 hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...

.

Function


Many cellular processes (DNA replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...

, transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...

, translation, recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...

, DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...

, ribosome biogenesis
Ribosome biogenesis
Ribosome biogenesis is the process of making ribosomes. In prokaryotic cells, it takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cell cytoplasm and in the nucleolus of eukaryotic cells...

) involve the separation of nucleic acid strands. Helicases are often utilized to separate strands of a DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 double helix or a self-annealed RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 molecule using the energy from ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

 hydrolysis, a process characterized by the breaking of hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...

s between annealed nucleotide bases
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...

. They move incrementally along one nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...

 strand of the duplex with a directionality
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...

 and processivity
Processivity
In molecular biology, processivity is a measure of the average number of nucleotides added by a DNA polymerase enzyme per association/disassociation with the template. DNA polymerases associated with DNA replication tend to be highly processive, while those associated with DNA repair tend to have...

 specific to each particular enzyme. There are many helicases (14 confirmed in E. coli, 24 in human cells) resulting from the great variety of processes in which strand separation must be catalyzed.

Helicases adopt different structures and oligomerization states. Whereas DnaB-like helicases unwind DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 as donut-shaped hexamer
Hexamer
A hexamer is a thing composed out of six sub-units.In microbiology, a hexamer is one of the proteins composing the polyhedral protein shell that encloses the bacterial micro-compartments known as carboxysomes....

s, other enzymes have been shown to be active as monomer
Monomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...

s or dimer
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...

s. Studies have shown that helicases may act passively, waiting for uncatalyzed unwinding to take place and then translocating between displaced strands, or can play an active role in catalyzing strand separation using the energy generated in ATP hydrolysis. In the latter case, the helicase acts comparably to an active motor, unwinding and translocating along its substrate as a direct result of its ATPase activity. Helicases may process much faster in vivo
In vivo
In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...

than in vitro
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...

due to the presence of accessory proteins that aid in the destabilization of the fork junction.

Defects in the gene that codes helicase cause Werner syndrome
Werner syndrome
Werner syndrome is a very rare, autosomal recessive disorder characterized by the appearance of premature aging....

, a disorder characterized by the appearance of premature aging.

Structural features


The common function of helicases accounts for the fact that they display a certain degree of amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

 sequence homology; they all possess common sequence motif
Sequence motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance...

s located in the interior of their primary sequence
Primary structure
The primary structure of peptides and proteins refers to the linear sequence of its amino acid structural units. The term "primary structure" was first coined by Linderstrøm-Lang in 1951...

. These are thought to be specifically involved in ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

 binding, ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

 hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...

 and translocation on the nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...

 substrate
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...

. The variable portion of the amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

 sequence is related to the specific features of each helicase.

Based on the presence of defined helicase motifs, it is possible to attribute a putative helicase activity to a given protein, though the presence of a motif does not confirm the protein as a helicase. Conserved motifs
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...

 do, however, support an evolutionary homology among enzymes. Based on the presence and the form of helicase motifs, helicases have been separated in 4 superfamilies and 2 smaller families. Some members of these families are indicated, with the organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

 from which they are extracted, and their function.

Superfamilies


Helicases have been classified in 6 superfamilies (SF1-SF6). All of the proteins bind ATP, and, as a consequence, all of them carry the classical Walker A
Walker motifs
The Walker A and Walker B motifs are protein sequence motifs. These were first reported in ATP-binding proteins by Walker and co-workers in 1982.-Walker A motif:...

 (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs.
  • Superfamily I: UvrD (E. coli, DNA repair), Rep (E. coli, DNA replication), PcrA
    PcrA
    PcrA, standing for plasmid copy reduced is a helicase that was originally discovered in a screen for chromosomally encoded genes that are affected in plasmid rolling circle replication in the Gram-positive pathogen Staphylococcus aureus....

     (Staphylococcus aureus
    Staphylococcus aureus
    Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium. It is frequently found as part of the normal skin flora on the skin and nasal passages. It is estimated that 20% of the human population are long-term carriers of S. aureus. S. aureus is the most common species of...

    , recombination), Dda
    Dda (DNA-dependent ATPase)
    Dda is the 439-amino acid 49,897-atomic mass unit protein coded by the Dda gene of the bacteriophage T4 phage, a virus that infects enterobacteria....

     (bacteriophage T4, replication initiation), RecD
    RecBCD
    RecBCD, also known as Exonuclease V, is an enzyme of the E. coli bacterium that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host of other factors...

     (E. coli, recombinational repair), TraI (F-plasmid, conjugative DNA transfer
    Bacterial conjugation
    Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells...

    ). This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in positive-strand single-stranded RNA viruses from superfamily 1. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.
  • Superfamily II: RecQ
    RecQ helicase
    RecQ helicase is a family of helicase enzymes that has been shown to be important in genome maintenance. They function through catalyzing the reaction ATP + H2O → ADP + P and thus driving the unwinding of paired DNA and translocating in the 3' to 5' direction...

     (E. coli, DNA repair), eIF4A (Baker's Yeast
    Saccharomyces cerevisiae
    Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...

    , RNA translation), WRN
    WRN (gene)
    WRN is a human gene that provides instructions for producing Werner protein, which is a type of enzyme called a helicase. Helicase enzymes generally unwind and separate double-stranded DNA. These activities are necessary before DNA can be copied in preparation for cell division...

     (human, DNA repair), NS3 (Hepatitis C
    Hepatitis C
    Hepatitis C is an infectious disease primarily affecting the liver, caused by the hepatitis C virus . The infection is often asymptomatic, but chronic infection can lead to scarring of the liver and ultimately to cirrhosis, which is generally apparent after many years...

     virus, replication). TRCF (Mfd) (E. coli, transcription-repair coupling).
  • Superfamily III: LTag (Simian Virus 40, replication), E1 (human papillomavirus
    Human papillomavirus
    Human papillomavirus is a member of the papillomavirus family of viruses that is capable of infecting humans. Like all papillomaviruses, HPVs establish productive infections only in keratinocytes of the skin or mucous membranes...

    , replication), Rep (Adeno-Associated Virus
    Adeno-associated virus
    Adeno-associated virus is a small virus which infects humans and some other primate species. AAV is not currently known to cause disease and consequently the virus causes a very mild immune response. AAV can infect both dividing and non-dividing cells and may incorporate its genome into that of...

    , replication, viral integration, virion packaging). Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori (origin of DNA replication) with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated.
  • DnaB-like family: dnaB
    DnaB helicase
    dnaB helicase is an enzyme in bacteria which opens the replication fork during DNA replication. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation...

     (E. coli, replication), gp41 (bacteriophage T4, DNA replication), T7gp4
    T7 DNA Helicase
    T7 DNA helicase is a hexameric motor protein that uses energy from dTTP hydrolysis to process unidirectionally along single stranded DNA, separating the two strands as it progresses.-Crystal structure:...

     (bacteriophage T7, DNA replication).
  • Rho-like family: Rho
    Rho factor
    A ρ factor is a prokaryotic protein involved in the termination of transcription.Rho factor is an essential transcription protein in prokaryotes. In Escherichia coli, it is a ~275 kD hexamer of identical subunits. Each subunit has an RNA-binding domain and an ATP-hydrolysis domain...

     (E. coli, transcription termination).


Note that these superfamilies do not subsume all possible helicases. For example, XPB
XPB
XPB is an ATP dependent human DNA helicase that is a part of the TFIIH transcription factor complex.-Structure:The 3D structure of the archeael homologue of XPB has been solved by X-ray crystallography by Dr...

 and ERCC2
ERCC2
ERCC2, or XPD is a protein involved in transcription-coupled nucleotide excision repair.The XPD gene encodes for a 2.3-kb mRNA containing 22 exons and 21 introns. The XPD protein is a 760 amino acids polypeptide with a size of 87kDa...

 are helicases not included in any of the above families.

RNA Helicases


RNA Helicases and DNA Helicases can be found together in all the Helicase Super Families except for SF6. However, not all RNA Helicases exhibit helicase activity as defined by enzymatic function, i.e., proteins of the Swi/Snf family. Although these proteins carry the typical helicase motifs, hydrolize ATP in a nucleic acid-dependent manner, and are built around a helicase core, in general, no unwinding activity is observed.

RNA Helicases that do exhibit unwinding activity have been characterized by at least two different mechanisms: canonical duplex unwinding and local strand separation. Canonical duplex unwinding is the stepwise directional separation of a duplex strand, as described above, for DNA unwinding. However, local strand separation occurs by a process wherein the helicase enzyme is loaded at any place along the duplex. This is usually aided by a single-stranded region of the RNA, and the loading of the enzyme is accompanied with ATP binding. Once the helicase and ATP are bound, local strand separation occurs, which requires binding of ATP but not the actual process of ATP hydrolysis. Presented with fewer base pairs the duplex then dissociates without further assistance from the enzyme. This mode of unwinding is used by DEAD-box helicases.

See also

  • chromodomain
    Chromodomain
    A chromodomain is a protein structural domain of about 40-50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin. The domain is highly conserved among both plants and animals, and is represented in a large number of different proteins in many...

     helicase DNA binding protein: CHD1
    CHD1
    Chromodomain-helicase-DNA-binding protein 1 is an enzyme that in humans is encoded by the CHD1 gene.-Interactions:CHD1 has been shown to interact with Nuclear receptor co-repressor 1.-Further reading:...

    , CHD1L
    CHD1L
    Chromodomain-helicase-DNA-binding protein 1-like is an enzyme that in humans is encoded by the CHD1L gene. It has been implicated in chromatin remodeling and DNA relaxation process required for DNA replication, repair and transcription....

    , CHD2
    CHD2
    Chromodomain-helicase-DNA-binding protein 2 is an enzyme that in humans is encoded by the CHD2 gene.-External links:...

    , CHD3
    CHD3
    Chromodomain-helicase-DNA-binding protein 3 is an enzyme that in humans is encoded by the CHD3 gene.-Interactions:CHD3 has been shown to interact with HDAC1, Histone deacetylase 2 and SERBP1.-Further reading:...

    , CHD4
    CHD4
    Chromodomain-helicase-DNA-binding protein 4 is an enzyme that in humans is encoded by the CHD4 gene.-Interactions:CHD4 has been shown to interact with HDAC1, Histone deacetylase 2, MTA2, SATB1 and Ataxia telangiectasia and Rad3 related....

    , CHD5
    CHD5
    Chromodomain-helicase-DNA-binding protein 5 is an enzyme that in humans is encoded by the CHD5 gene.-Further reading:...

    , CHD6, CHD7
    CHD7
    Chromodomain-helicase-DNA-binding protein 7 also known as ATP-dependent helicase CHD7 is an enzyme that in humans is encoded by the CHD7 gene....

    , CHD8
    CHD8
    Chromodomain-helicase-DNA-binding protein 8 is an enzyme that in humans is encoded by the CHD8 gene.-Further reading:...

    , CHD9
    CHD9
    Chromodomain-helicase-DNA-binding protein 9 is an enzyme that in humans is encoded by the CHD9 gene.-Further reading:...

  • DEAD box
    DEAD box
    DEAD box proteins are involved in an assortment of metabolic processes that involve RNA. They are highly conserved in nine domains and can be found in both prokaryotes and eukaryotes, but not all...

    /DEAD/DEAH box helicase
    DEAD/DEAH box helicase
    The DEAD/DEAH box helicases are a family of proteins whose purpose is to unwind nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and...

    : DDX3X
    DDX3X
    ATP-dependent RNA helicase DDX3X is an enzyme that in humans is encoded by the DDX3X gene.-Further reading:...

    , DDX5
    DDX5
    Probable ATP-dependent RNA helicase DDX5 also known as DEAD box protein 5 or RNA helicase p68 is an enzyme that in humans is encoded by the DDX5 gene.- Function :...

    , DDX6
    DDX6
    Probable ATP-dependent RNA helicase DDX6 is an enzyme that in humans is encoded by the DDX6 gene.-Further reading:...

    , DDX10
    DDX10
    Probable ATP-dependent RNA helicase DDX10 is an enzyme that in humans is encoded by the DDX10 gene.-Further reading:...

    , DDX11
    DDX11
    Probable ATP-dependent RNA helicase DDX11 is an enzyme that in humans is encoded by the DDX11 gene.-Further reading:...

    , DDX12, DDX58
    DDX58
    Probable ATP-dependent RNA helicase DDX58 is an enzyme that in humans is encoded by the DDX58 gene. It codes for a protein called retinoic acid-inducible gene 1 protein , also known as DEAD-box protein 58 , which is a cell receptor found in the cytoplasm of cells...

    , DHX8, DHX9
    DHX9
    ATP-dependent RNA helicase A is an enzyme that in humans is encoded by the DHX9 gene.-Interactions:...

    , DHX37, DHX40, DHX58
    DHX58
    Probable ATP-dependent RNA helicase DHX58, also called LGP2 , is an enzyme that in humans is encoded by the DHX58 gene. It is speculated that LGP2 is a negative regulator of host innate immune defense against viruses. The repressor domain of DHX58 interacts with DDX58 and negatively regulates...

  • ASCC3
    ASCC3
    Activating signal cointegrator 1 complex subunit 3 is a protein that in humans is encoded by the ASCC3 gene.-Interactions:ASCC3 has been shown to interact with RELA, C-jun and Serum response factor.-Further reading:...

    , BLM, BRIP1
    BRIP1
    Fanconi anemia group J protein is a protein that in humans is encoded by the BRCA1-interacting protein 1 gene.This protein also appears to be important in ovarian cancer where it seems to act as an antioncogene.-Further reading:...

    , DNA2, FBXO18, FBXO30, HELB, HELLS
    HELLS
    Lymphoid-specific helicase is an enzyme that in humans is encoded by the HELLS gene.-Further reading:...

    , HELQ, HELZ, HFM1, HLTF
    HLTF
    Helicase-like transcription factor is an enzyme that in humans is encoded by the HLTF gene.-Interactions:HLTF has been shown to interact with UBE2N, RAD18 and UBE2V2.-Further reading:...

    , IFIH1
    IFIH1
    Interferon-induced helicase C domain-containing protein 1, also known as MDA5 , is an enzyme that in humans is encoded by the IFIH1 gene...

    , NAV2
    NAV2
    Neuron navigator 2 is a protein that in humans is encoded by the NAV2 gene.-Further reading:...

    , PIF1, RECQL
    RECQL
    ATP-dependent DNA helicase Q1 is an enzyme that in humans is encoded by the RECQL gene.-Interactions:RECQL has been shown to interact with KPNA4 and Karyopherin alpha 2.-Further reading:...

    , RTEL1, SHPRH
    SHPRH
    E3 ubiquitin-protein ligase SHPRH is an enzyme that in humans is encoded by the SHPRH gene.-Further reading:...

    , SMARCA4
    SMARCA4
    Transcription activator BRG1 also known as ATP-dependent helicase SMARCA4 is a protein that in humans is encoded by the SMARCA4 gene.- Function :...

    , SMARCAL1
    SMARCAL1
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 is a protein that in humans is encoded by the SMARCAL1 gene.-External links:*-Further reading:...

    , WRN
    WRN (gene)
    WRN is a human gene that provides instructions for producing Werner protein, which is a type of enzyme called a helicase. Helicase enzymes generally unwind and separate double-stranded DNA. These activities are necessary before DNA can be copied in preparation for cell division...

    , WRNIP1
    WRNIP1
    ATPase WRNIP1 is an enzyme that in humans is encoded by the WRNIP1 gene.-Interactions:WRNIP1 has been shown to interact with Werner syndrome ATP-dependent helicase.-External links:...