Structure of E. coli helicase RuvA

Helicases are a class of enzymes vital to all living organisms. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i. A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a Phosphate group and two other Molecules over two Annealing, in Genetics, means for DNA or RNA to pair by Hydrogen bonds to a complementary sequence, forming a double-stranded e. DNA, RNA, or RNA-DNA hybrid) using energy derived from nucleotide hydrolysis. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Hydrolysis is a Chemical reaction during which one or more water molecules are split into hydrogen and hydroxide ions which may go on to participate in further reactions

Function

Many cellular processes (DNA replication, transcription, translation, recombination, DNA repair, ribosome biogenesis) involve the separation of nucleic acid strands. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Genetic recombination is the process by which a strand of genetic material (usually DNA; but can also be RNA) is broken and then joined to a different DNA molecule DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its Genome. 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 Helicases are often utilized to separate strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP or GTP hydrolysis, a process characterized by the breaking of hydrogen bonds between annealed nucleotide bases. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known In Geometry a double helix (plural helices) typically consists of two congruent helices with the same axis differing by a translation Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy Guanosine-5'-triphosphate ( GTP) is a Purine Nucleotide. One role is as substrate for the synthesis of RNA during transcription. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called They move incrementally along one nucleic acid strand of the duplex with a directionality and processivity specific to each particular enzyme. A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid. In Molecular biology, processivity is a measure of the average number of Nucleotides added by a DNA polymerase Enzyme per association/disassociation 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. In Chemistry, an oligomer consists of a limited number of Monomer units (ολιγος or oligos is Greek for "a few" in contrast to a Whereas DnaB-like helicases unwind DNA as donut shaped hexamers, other enzymes have been shown to be active as monomers or dimers. DnaB helicase is an enzyme in Bacteria which opens the Replication fork during DNA replication. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known In Chemistry, an oligomer consists of a limited number of Monomer units (ολιγος or oligos is Greek for "a few" in contrast to a A monomer (from Greek mono "one" and meros "part" is a small Molecule that may become chemically bonded to other A dimer is a Chemical or Biological entity consisting of two subunits called Monomers which are held together by either Intramolecular forces Recent studies showed that helicases do not merely wait passively for the fork to widen, but play an active role in forcing the fork to open,^[1] thus it is an active motor unwinding its substrate^[2]. The replication fork is a structure that forms during DNA replication. Helicases may process much faster in vivo than in vitro due to the presence of accessory proteins that aid in the destabilization of the fork junction. In vivo ( Latin: within the living means that which takes place inside an organism. In vitro ( Latin: within the glass refers to the technique of performing a given experiment in a controlled environment outside of a living Organism ^[2]

Structural features

The common function of helicases accounts for the fact that they display a certain degree of amino acid sequence homology; they all possess common sequence motifs located in the interior of their primary sequence. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this In Evolutionary biology, homology has come to mean any similarity between characters that is due to their shared ancestry. 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 In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including These are thought to be specifically involved in ATP binding, ATP hydrolysis and translocation on the nucleic acid substrate. Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy Hydrolysis is a Chemical reaction during which one or more water molecules are split into hydrogen and hydroxide ions which may go on to participate in further reactions A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information The variable portion of the amino acid sequence is related to the specific features of each helicase. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this

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 do, however, support an evolutionary homology among enzymes. In Biology, conserved sequences are similar or identical sequences that may occur within Nucleic acids Proteins or polymeric carbohydrates 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 from which they are extracted, and their function.

Superfamilies

• Superfamily I: UvrD (E. coli, DNA repair), Rep (E. coli, DNA replication), PcrA (Staphylococcus aureus, recombination), Dda (bacteriophage T4, replication initiation). Staphylococcus aureus (ˌstæfɨləˈkɒkəs ˈɔriəs literally "Golden Cluster Seed" and also known as golden staph) is the most common cause of
• Superfamily II: RecQ (E. RecQ helicase is a family of Helicase Enzymes that has been shown to be important in genome maintenance coli, DNA repair), eIF4A (Baker's Yeast, RNA translation), WRN (human, DNA repair), NS3^[3] (Hepatitis C virus, replication). Saccharomyces cerevisiae is a Species of Budding Yeast. It is perhaps the most useful Yeast owing to its use since ancient times WRN ( Werner syndrome) is a Human Gene that provides instructions for producing Werner protein, which is a type of Enzyme called a Hepatitis C is a blood-borne infectious disease that is caused by the Hepatitis C virus ( HCV) affecting the Liver. TRCF (Mfd) (E. coli, transcription-repair coupling).
• Superfamily III: LTag (Simian Virus 40, replication), E1 (human papillomavirus, replication), Rep (Adeno-Associated Virus, replication, viral integration, virion packaging). SV40 is an abbreviation for Simian vacuolating virus 40 or Simian virus 40, a Polyomavirus that is found in both Monkeys and A human papillomavirus ( HPV) is a Papillomavirus that infects the skin and Mucous membranes of Humans Approximately 130 HPV types have been Adeno-associated virus (AAV is a small Virus which infects humans and some other primate species
• DnaB-like family: dnaB (E. DnaB helicase is an enzyme in Bacteria which opens the Replication fork during DNA replication. coli, replication), gp41 (bacteriophage T4, DNA replication),T7gp4 (bacteriophage T7, DNA replication). Enterobacteria phage T4 is a Phage that infects E coli bacteria. T7 DNA Helicase is a hexameric motor protein that uses energy from dTTP Hydrolysis to process unidirectionally along single stranded DNA, separating the
• Rho-like family: Rho (E. coli, transcription termination).

References

1. ^ Johnson DS, Bai L, Smith BY, Patel SS, Wang MD (2007). "Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped t7 helicase". Cell 129 (7): 1299-309. doi:10.1016/j.cell.2007.04.038. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document. PMID 17604719.  
2. ^ ^{a b} Researchers solve mystery of how DNA strands separate (2007-07-03). Year 2007 ( MMVII) was a Common year starting on Monday of the Gregorian calendar in the 21st century. Events 324 - Battle of Adrianople Constantine I defeats Licinius, who flees to Byzantium. Retrieved on 2007-07-05. Year 2007 ( MMVII) was a Common year starting on Monday of the Gregorian calendar in the 21st century. Events 1295 - Scotland and France form an alliance the beginnings of the Auld Alliance, against England.
3. ^ Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco Jr I, Pylr AM, Bustamante C, "RNA Translocation and Unwinding Mechanism of HCV NS3 Helicase and its Coordination by ATP", Nature. Carlos José Bustamante (born 1951 in Lima, Peru) is an American Scientist. Nature is a prominent Scientific journal, first published on 4 November 1869 2006 Jan 5; 439: 105-108.

• Anand SP, Zheng H, Bianco PR, Leuba SH, Khan SA. DNA helicase activity of PcrA is not required for displacement of RecA protein from DNA or inhibition of RecA-mediated DNA strand exchange. Journal of Bacteriology (2007) 189 (12):4502-4509.
• Bird L, Subramanya HS, Wigley DB, "Helicases: a unifying structural theme?", Current Opinion in Structural Biology. 1998 Feb; 8 (1): 14-18.
• Betterton MD, Julicher F, "Opening of nucleic-acid double strands by helicases: active versus passive opening.", Physical Review E. Physical Review (frequently abbreviated as Phys Rev) is one of the oldest and most-respected Scientific journals publishing research on all aspects of 2005 Jan; 71 (1): 011904.

External links

• MeSH DNA+Helicases
• MeSH RNA+Helicases