![DNA polymerase III (with subunits)](https://upload.wikimedia.org/wikipedia/commons/a/a2/DNA_polymerase_III_%28with_subunits%29.jpg)
DNA polymerase III holoenzyme is the primary
enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...
complex involved in
prokaryotic
A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
. It was discovered by
Thomas Kornberg (son of
Arthur Kornberg
Arthur Kornberg (March 3, 1918 – October 26, 2007) was an American biochemist who won the Nobel Prize in Physiology or Medicine 1959 for the discovery of "the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic ac ...
) and
Malcolm Gefter in 1970. The complex has high processivity (i.e. the number of
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
s added per binding event) and, specifically referring to the replication of the ''
E.coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Esche ...
''
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
, works in conjunction with four other DNA polymerases (
Pol I
DNA polymerase I (or Pol I) is an enzyme that participates in the process of prokaryotic DNA replication. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase (and the first known of any kind of polymerase). It was initia ...
,
Pol II,
Pol IV, and
Pol V
DNA Polymerase V (Pol V) is a polymerase enzyme involved in DNA repair mechanisms in bacteria, such as ''Escherichia coli''. It is composed of a UmuD' homodimer and a UmuC monomer, forming the UmuD'2C protein complex. It is part of the Y-family o ...
). Being the primary
holoenzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as product (ch ...
involved in replication activity, the DNA Pol III
holoenzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as product (ch ...
also has proofreading capabilities that corrects replication mistakes by means of
exonuclease
Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is the ...
activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the
replisome
The replisome is a complex molecular machine that carries out replication of DNA. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthe ...
, which is located at the replication fork.
Components
The replisome is composed of the following:
*2 DNA Pol III enzymes, each comprising α, ε and θ subunits. (It has been proven that there is a third copy of Pol III at the replisome.
)
**the α subunit (encoded by the
dnaE
DnaE, the gene product of ''dnaE'', is the catalytic α subunit of DNA polymerase III, acting as a DNA polymerase. This enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules u ...
gene) has the polymerase activity.
**the ε subunit (
dnaQ
''dnaQ'' is the gene encoding the ε subunit of DNA polymerase III in ''Escherichia coli''. The ε subunit is one of three core proteins in the DNA polymerase complex. It functions as a 3’→5’ DNA directed proofreading exonuclease that remove ...
) has 3'→5' exonuclease activity.
**the θ subunit (
holE
A hole is an opening in or through a particular medium, usually a solid body. Holes occur through natural and artificial processes, and may be useful for various purposes, or may represent a problem needing to be addressed in many fields of en ...
) stimulates the ε subunit's proofreading.
*2 β units (
dnaN
dnaN is the gene that codes for the DNA clamp (also known as β sliding clamp) of DNA polymerase III in prokaryotes. The β clamp physically locks Pol III onto a DNA strand during replication to help increase its processivity. The eukaryotic equiv ...
) which act as sliding
DNA clamp
A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents ...
s, they keep the polymerase bound to the DNA.
*2 τ units (
dnaX
The τ and γ subunits are part of the DNA polymerase III holoenzyme
DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg (son of Arthur Kornberg) and Malc ...
) which act to dimerize two of the core enzymes (α, ε, and θ subunits).
*1 γ unit (also dnaX) which acts as a clamp loader for the lagging strand
Okazaki fragment
Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA ...
s, helping the two β subunits to form a unit and bind to DNA. The γ unit is made up of 5 γ subunits which include 3 γ subunits, 1 δ subunit (
holA
In molecular biology, the δ (delta) subunit of DNA polymerase III is encoded by the holA gene in ''E. coli'' and other bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biolo ...
), and 1 δ' subunit (
holB
In '' E. coli'' and other bacteria, holB is a gene that encodes the delta prime subunit of DNA polymerase III
DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Korn ...
). The δ is involved in copying of the lagging strand.
* Χ (
holC
In '' E. coli'' and other bacteria, holC is a gene that encodes the chi subunit of DNA polymerase III
DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas B. Kornberg, ...
) and Ψ (
holD
Hold may refer to:
Physical spaces
* Hold (ship), interior cargo space
* Baggage hold, cargo space on an airplane
* Stronghold, a castle or other fortified place
Arts, entertainment, and media
* Hold (musical term), a pause, also called a Fermat ...
) which form a 1:1 complex and bind to γ or τ. X can also mediate the switch from RNA primer to DNA.
Activity
DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second.
DNA Pol III activity begins after strand separation at the origin of replication. Because DNA synthesis cannot start ''de novo'', an
RNA primer
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in Genetic code, coding, Translation (biology), decoding, Regulatory RNA, regulation and Gene expression, expression of genes. RNA and deoxyribonucleic acid ( ...
, complementary to part of the single-stranded DNA, is synthesized by
primase
DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA (or DNA in some
living organisms) segment called a primer complementary to a ssDNA (single-stranded ...
(an
RNA polymerase
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template.
Using the enzyme helicase, RNAP locally opens the ...
):
("!" for
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
, '"$" for
DNA, "*" for
polymerase
A polymerase is an enzyme ( EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base- ...
)
-------->
* * * *
! ! ! ! _ _ _ _
_ _ _ _ ,
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
, <--
ribose
Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compo ...
(sugar)-phosphate backbone
G U A U ,
Pol , <--
RNA primer
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in Genetic code, coding, Translation (biology), decoding, Regulatory RNA, regulation and Gene expression, expression of genes. RNA and deoxyribonucleic acid ( ...
* * * * , _ _ _ _, <--hydrogen bonding
C A T A G C A T C C <--
template
Template may refer to:
Tools
* Die (manufacturing), used to cut or shape material
* Mold, in a molding process
* Stencil, a pattern or overlay used in graphic arts (drawing, painting, etc.) and sewing to replicate letters, shapes or designs
Co ...
ss
DNA (single-stranded
DNA)
_ _ _ _ _ _ _ _ _ _ <--
deoxyribose
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone
$ $ $ $ $ $ $ $ $ $
Addition onto 3'OH
As replication progresses and the
replisome
The replisome is a complex molecular machine that carries out replication of DNA. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthe ...
moves forward, DNA polymerase III arrives at the RNA primer and begins replicating the DNA, adding onto the 3'OH of the primer:
* * * *
! ! ! ! _ _ _ _
_ _ _ _ ,
DNA , <--
deoxyribose
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone
G U A U ,
Pol , <--
RNA primer
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in Genetic code, coding, Translation (biology), decoding, Regulatory RNA, regulation and Gene expression, expression of genes. RNA and deoxyribonucleic acid ( ...
* * * * , _III_ _, <--hydrogen bonding
C A T A G C A T C C <--
template
Template may refer to:
Tools
* Die (manufacturing), used to cut or shape material
* Mold, in a molding process
* Stencil, a pattern or overlay used in graphic arts (drawing, painting, etc.) and sewing to replicate letters, shapes or designs
Co ...
ss
DNA (single-stranded
DNA)
_ _ _ _ _ _ _ _ _ _ <--
deoxyribose
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone
$ $ $ $ $ $ $ $ $ $
Synthesis of DNA
DNA polymerase III will then synthesize a continuous or discontinuous strand of DNA, depending if this is occurring on the leading or lagging strand (
Okazaki fragment
Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA ...
) of the DNA. DNA polymerase III has a high processivity and therefore, synthesizes DNA very quickly. This high processivity is due in part to the β-clamps that "hold" onto the DNA strands.
----------->
* * * *
! ! ! ! $ $ $ $ $ $ _ _ _ _
_ _ _ _ _ _ _ _ _ _,
DNA , <--
deoxyribose
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone
G U A U C G T A G G,
Pol , <--
RNA primer
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in Genetic code, coding, Translation (biology), decoding, Regulatory RNA, regulation and Gene expression, expression of genes. RNA and deoxyribonucleic acid ( ...
* * * * * * * * * *, _III_ _, <--hydrogen bonding
C A T A G C A T C C <--
template
Template may refer to:
Tools
* Die (manufacturing), used to cut or shape material
* Mold, in a molding process
* Stencil, a pattern or overlay used in graphic arts (drawing, painting, etc.) and sewing to replicate letters, shapes or designs
Co ...
ss
DNA (single-stranded
DNA)
_ _ _ _ _ _ _ _ _ _ <--
deoxyribose
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone
$ $ $ $ $ $ $ $ $ $
Removal of primer
After replication of the desired region, the RNA primer is removed by
DNA polymerase I
DNA polymerase I (or Pol I) is an enzyme that participates in the process of prokaryotic DNA replication. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase (and the first known of any kind of polymerase). It was initiall ...
via the process of
nick translation
Nick translation (or head translation), developed in 1977 by Peter Rigby and Paul Berg, is a tagging technique in molecular biology in which DNA Polymerase I is used to replace some of the nucleotides of a DNA sequence with their labeled analogu ...
. The removal of the RNA primer allows
DNA ligase
DNA ligase is a specific type of enzyme, a ligase, () that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organ ...
to ligate the DNA-DNA nick between the new fragment and the previous strand. DNA polymerase I & III, along with many other enzymes are all required for the high fidelity, high-processivity of DNA replication.
See also
*
Beta clamp
A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents ...
*
DNA polymerase
A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...
*
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
References
External links
Overviewat
Oregon State University
Oregon State University (OSU) is a public land-grant, research university in Corvallis, Oregon. OSU offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees. It has the 10th largest engineering co ...
*
Clamping down on pathogenic bacteria– how to shut down a key DNA polymerase complex
{{Portal bar, Biology, border=no
EC 2.7.7
DNA replication
Enzymes
Protein complexes