DnaA
Encyclopedia
dnaA is a replication initiation factor which promotes the unwinding or denaturation
of DNA
at oriC (around 240bp
in Escherichia coli
), during DNA replication
in prokaryotes.
The formation of the oriC/DnaA complex and DNA unwinding requires ATP hydrolysis
.
The oriC site in E. coli has three AT
rich 13 base pair
regions (DUE's elements) followed by five 9 bp regions. Around 10 dnaA molecule
s bind to the 9 bp regions, which wrap around the proteins causing the DNA
at the AT-rich region to unwind. There are 8 dnaA binding sites within oriC, which dnaA binds with differential affinity. When DNA replication is about to commence, dnaA occupies all of the high and low affinity binding sites. The denatured AT-rich region allows for the recruitment of DnaB (helicase
) complexes with DnaC
(helicase loader). DnaC helps the helicase to bind to and to properly accommodate the ssDNA at the 13 bp region, this is accomplished by ATP
hydrolysis
after which DnaC is released. Single-strand binding protein's
(SSBs) stabilize the single DNA strands in order to maintain the replication bubble. DnaB is a 5'->3' helicase, so it travels on the lagging strand. It associates with DnaG
(a primase
) to form the only primer
for the leading strand and to add RNA
primers on the lagging strand. The interaction between DnaG and DnaB is necessary to control the longitude of Okazaki fragments on the lagging strand. DNA polymerase III is then able to start DNA replication
.
DnaA contains two conserved
regions: the first is located in the central part of the protein and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding.
Denaturation (biochemistry)
Denaturation is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent , or heat...
of 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...
at oriC (around 240bp
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...
in Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
), during 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...
in prokaryotes.
The formation of the oriC/DnaA complex and DNA unwinding requires ATP hydrolysis
ATP hydrolysis
ATP hydrolysis is the reaction by which chemical energy that has been stored and transported in the high-energy phosphoanhydridic bonds in ATP is released, for example in the muscles, to produce work. The product is ADP and an inorganic phosphate, orthophosphate...
.
The oriC site in E. coli has three AT
Threonine
Threonine is an α-amino acid with the chemical formula HO2CCHCHCH3. Its codons are ACU, ACA, ACC, and ACG. This essential amino acid is classified as polar...
rich 13 base pair
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...
regions (DUE's elements) followed by five 9 bp regions. Around 10 dnaA molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
s bind to the 9 bp regions, which wrap around the proteins causing the 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...
at the AT-rich region to unwind. There are 8 dnaA binding sites within oriC, which dnaA binds with differential affinity. When DNA replication is about to commence, dnaA occupies all of the high and low affinity binding sites. The denatured AT-rich region allows for the recruitment of DnaB (helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
) complexes with DnaC
DnaC
dnaC is a bacterial gene that codes for protein DnaC. DnaC, also known as the helicase loader, is a regulator of DnaB. DnaC forms a complex with DnaB, thus enabling DnaB to perform its functions in bacterial DNA replication. This interaction of DnaC with DnaB requires the hydrolysis of ATP....
(helicase loader). DnaC helps the helicase to bind to and to properly accommodate the ssDNA at the 13 bp region, this is accomplished by 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...
after which DnaC is released. Single-strand binding protein's
Single-strand binding protein
Single-strand binding protein, also known as SSB or SSBP, binds to single stranded regions of DNA to prevent premature annealing. The strands have a natural tendency to revert to the duplex form, but SSB binds to the single strands, keeping them separate and allowing the DNA replication machinery...
(SSBs) stabilize the single DNA strands in order to maintain the replication bubble. DnaB is a 5'->3' helicase, so it travels on the lagging strand. It associates with DnaG
DnaG
DnaG is a bacterial primase which synthesizes short RNA oligonucleotides during DNA replication. These RNA oligonucleotides serve as primers for DNA synthesis by bacterial DNA polymerase Pol III. On one of the two parental strands, called the lagging strand, the primase makes a primer every few...
(a primase
Primase
DNA primase is an enzyme involved in the replication of DNA.Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template...
) to form the only primer
Primer (molecular biology)
A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...
for the leading strand and to add RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
primers on the lagging strand. The interaction between DnaG and DnaB is necessary to control the longitude of Okazaki fragments on the lagging strand. DNA polymerase III is then able to start 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...
.
DnaA contains two conserved
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...
regions: the first is located in the central part of the protein and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding.