DNA polymerase: Difference between revisions
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==Overview== | ==Overview== | ||
'''DNA polymerases''' are enzymes that play a key role in [[DNA]] replication. '''DNA replication''' is the process of splitting an existing double-stranded DNA molecule into two single strands of DNA, then using DNA polymerases to translate the single strands. The process of translation results in the creation of the '''complementary''' DNA strands and results in the creation of two double-stranded DNA molecules that are exact replicas of the original DNA molecule. The complementary strands are created in the 5'-3' direction. Certain DNA polymerases are also responsible for proofreading the newly synthesized DNA strand and using exonuclease to remove and replace any errors that occurred. DNA polymerases are divided into 7 families according to their sequence homology and 3D structure similarities.<ref>PMID:10364165</ref> The families are: | '''DNA polymerases''' are enzymes that play a key role in [[DNA]] replication. '''DNA replication''' is the process of splitting an existing double-stranded DNA molecule into two single strands of DNA, then using DNA polymerases to translate the single strands. The process of translation results in the creation of the '''complementary''' DNA strands and results in the creation of two double-stranded DNA molecules that are exact replicas of the original DNA molecule. The complementary strands are created in the 5'-3' direction. Certain DNA polymerases are also responsible for proofreading the newly synthesized DNA strand and using exonuclease to remove and replace any errors that occurred. DNA polymerases are divided into 7 families according to their sequence homology and 3D structure similarities.<ref name='SteitzJBiolChem1999'>PMID:10364165</ref> The families are: | ||
* Family A - DNA replication and repair ( | * Family A - DNA replication and repair (DNA Polymerase I, γ) | ||
* Family B - DNA replication and repair ( | * Family B - DNA replication and repair (DNA Polymerase II, α, δ, ε). See [[DNA Polymerase in Thermococcus gorgonarius]]. | ||
* Family C - DNA replication in prokaryotes ( | * Family C - DNA replication in prokaryotes (DNA Polymerase III) | ||
* Family D - DNA replication in archaea | * Family D - DNA replication in archaea | ||
* Family X - DNA repair in eukaryotes ( | * Family X - DNA repair in eukaryotes (DNA Polymerase β, λ, μ) | ||
* Family Y - DNA replication of damaged DNA ( | * Family Y - DNA replication of damaged DNA (DNA Polymerase IV, V, η, ι, κ) | ||
* Family RT - reverse transcriptase (See [[Reverse transcriptase]].) | * Family RT - reverse transcriptase (See [[Reverse transcriptase]].) | ||
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DNA polymerases are some of the most accurate enzymes and have about one mistake for every one billion copies. When a mistake is made, many of the DNA polymerases have the ability to proofread the newly synthesized DNA and correct any mistakes made during replication. The enzymes proofread in the 5'-3' direction. When an error is found, the misplaced nucleotide is cut out so the correct nucleotide can be inserted. This process is often referred to as '''5'-3'exonuclease activity'''. | DNA polymerases are some of the most accurate enzymes and have about one mistake for every one billion copies. When a mistake is made, many of the DNA polymerases have the ability to proofread the newly synthesized DNA and correct any mistakes made during replication. The enzymes proofread in the 5'-3' direction. When an error is found, the misplaced nucleotide is cut out so the correct nucleotide can be inserted. This process is often referred to as '''5'-3'exonuclease activity'''. | ||
==Disease== | |||
Viral DNA polymerase is inhibited by [[Aciclovir]] which is used for treatment of various viral infections. | |||
==Types of DNA Polymerase== | ==Types of DNA Polymerase== | ||
According to their sequence homology and 3D structure similarities, DNA Polymerases can be divided into 7 families: A, B, C, D, X, Y, and RT | According to their sequence homology and 3D structure similarities, DNA Polymerases can be divided into 7 families: A, B, C, D, X, Y, and RT <ref name='SteitzJBiolChem1999'/>. | ||
{| class="wikitable" | {| class="wikitable" | ||
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====Family X==== | ====Family X==== | ||
Family X polymerases consist of polymerases like Pol β, Pol μ, and Pol λ. Pol β's main function is short-patch base excision repair, a repair pathway used for repairing alkylated or oxidized bases. Pol λ and Pol μ are essential for rejoining DNA double-strand breaks due to hydrogen peroxide and ionizing radiation, respectively.<ref name="ncbi" /> For more details see [[DNA polymerase beta]]. | Family X polymerases consist of polymerases like Pol β, Pol μ, and Pol λ. Pol β's main function is short-patch base excision repair, a repair pathway used for repairing alkylated or oxidized bases. Pol λ and Pol μ are essential for rejoining DNA double-strand breaks due to hydrogen peroxide and ionizing radiation, respectively.<ref name="ncbi" /> For more details see [[DNA polymerase beta]] and [[DNA Polymerase beta (hebrew)]]. | ||
====Polymerases η, Polymerase ι, and Polymerase κ==== | ====Polymerases η, Polymerase ι, and Polymerase κ==== | ||
Polymerase η, Polymerase ι, and Polymerase κ are Family Y DNA polymerases involved in the DNA repair by '''translesion synthesis'''. Polymerases in Family Y are prone to errors during DNA synthesis. Pol η is important for the accurate translesion synthesis of DNA damage resulting from ultraviolet radiation. The function of Pol κ is not completely understood, but it is thought to act as an extender or inserter of a specific base at certain DNA lesions. All three translesion synthesis polymerases are activated by stalled replicative DNA polymerases.<ref name="ncbi" /> | Polymerase η, Polymerase ι, and Polymerase κ are Family Y DNA polymerases involved in the DNA repair by '''translesion synthesis'''. Polymerases in Family Y are prone to errors during DNA synthesis. Pol η is important for the accurate translesion synthesis of DNA damage resulting from ultraviolet radiation. The function of Pol κ is not completely understood, but it is thought to act as an extender or inserter of a specific base at certain DNA lesions. All three translesion synthesis polymerases are activated by stalled replicative DNA polymerases.<ref name="ncbi" /> | ||
====Polymerase θ see [[DNA Polymerase Theta]]==== | |||
====Terminal deoxynucleotidyl transferase==== | |||
TdT catalyzes the polymerization of deoxynucleoside triphophates to the 3'-hydroxyl group of preformed polynucleotide chain. TdT is a non-template directed DNA polymerase and was detected in thymus glands<ref>PMID:12170602</ref>. | |||
===Prokaryotic Polymerase=== | ===Prokaryotic Polymerase=== | ||
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====DNA Polymerase I==== | ====DNA Polymerase I==== | ||
[[DNA Polymerase I]] is a family A enzyme whose main function is excision repair of DNA strands through 3'-5' and 5'-3' exonuclease. This polymerase also helps with Okazaki fragment maturation. '''Okazaki fragments''' are short synthesized strands of DNA that form the lagging strand during DNA replication. When Polymerase I does replicate, it starts adding nucleotides at the RNA primer and moves in the 5'-3' direction. This polymerase is also the major polymerase in ''E. coli''.<ref name="ncbi" /> See also [[Taq DNA polymerase (Hebrew)]]. | [[DNA Polymerase I]] is a family A enzyme whose main function is excision repair of DNA strands through 3'-5' and 5'-3' exonuclease. This polymerase also helps with Okazaki fragment maturation. '''Okazaki fragments''' are short synthesized strands of DNA that form the lagging strand during DNA replication. When Polymerase I does replicate, it starts adding nucleotides at the RNA primer and moves in the 5'-3' direction. This polymerase is also the major polymerase in ''E. coli''.<ref name="ncbi" /> See also [[Taq DNA polymerase (Hebrew)]]. | ||
<scene name='44/440019/Cv/ | <scene name='44/440019/Cv/6'>Octylglucoside binding site</scene> in Family A DNA polymerase I ([[1taq]]). | ||
<scene name='44/440019/Cv/7'>Zn coordination site contains 3 Asp residues</scene> in Family A DNA polymerase I ([[1taq]]).<ref>PMID:7637814</ref> | |||
See also [[Vibriophage phiVC8 DpoZ]] | |||
====DNA Polymerase II==== | ====DNA Polymerase II==== | ||
DNA polymerase II belongs to family B. It is responsible for 3'-5' exonuclease activity and restarting replication after the synthesis process has stopped due to damage in the DNA strand. Polymerase II is located at the replication fork in order to help direct the activity of other polymerases.<ref name="ncbi" /> | DNA polymerase II belongs to family B. It is responsible for 3'-5' exonuclease activity and restarting replication after the synthesis process has stopped due to damage in the DNA strand. Polymerase II is located at the replication fork in order to help direct the activity of other polymerases.<ref name="ncbi" /> | ||
====DNA Polymerase III==== | ====DNA Polymerase III==== | ||
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====DNA Polymerase IV==== | ====DNA Polymerase IV==== | ||
DNA polymerase IV is involved in '''non-targeted mutagenesis'''. Belonging to family Y, this enzyme is activated when synthesis at the replication fork stalls. once activated, Polymerase IV creates a checkpoint, stops replication, and allows time to properly repair lesions in the DNA strand. Polymerase IV is also involved in '''translesion synthesis''', a DNA repair mechanism. However, the enzyme lacks nuclease activity making it prone to errors in DNA replication.<ref name="ncbi" /> | DNA polymerase IV is involved in '''non-targeted mutagenesis'''. Belonging to family Y, this enzyme is activated when synthesis at the replication fork stalls. once activated, Polymerase IV creates a checkpoint, stops replication, and allows time to properly repair lesions in the DNA strand. Polymerase IV is also involved in '''translesion synthesis''', a DNA repair mechanism. However, the enzyme lacks nuclease activity making it prone to errors in DNA replication.<ref name="ncbi" /> | ||
====DNA Polymerase V==== | ====DNA Polymerase V==== | ||
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===Reverse Transcriptase=== | ===Reverse Transcriptase=== | ||
The most commonly known Reverse Transcriptase DNA polymerase is HIV-1 Reverse Transcriptase. The reason this is so important to understand is that it is the target of anti-AIDS drugs. <ref>PMID: 7526780</ref> For detailed information on the RT family polymerases, see [[Reverse transcriptase]]. | |||
==Structure== | ==Structure== | ||
The basic structure of all DNA polymerases consists of subdomains referred to as the palm, fingers, and thumb. The palm contains catalytically essential amino acids in it's active sites. The fingers are essential for nucleotide recognition and binding. The thumb is important for the binding of the DNA substrate. These subdomains, along with other subdomains specific to each family, are essential for the correct functioning of DNA polymerase. | The basic structure of all DNA polymerases consists of subdomains referred to as the palm, fingers, and thumb and resemble an open right hand. The palm contains catalytically essential amino acids in it's active sites. The fingers are essential for nucleotide recognition and binding. The thumb is important for the binding of the DNA substrate. Between the finger and thumb domains is a pocket that is made up of two regions; the insertion site and postinsertion site. The incoming nucleotides bind to the insertion site and the new base pair resides in the postinsertion site. These subdomains, along with other subdomains specific to each family, are essential for the correct functioning of DNA polymerase. The structures of each of these subdomains are slightly different for each polymerases; to view these structures in greater detail, refer to the links at the bottom of the page. <ref name="structure">PMID: 16230118</ref> | ||
===Family A=== | ===Family A=== | ||
In addition to the basic structure of DNA polymerase, the Family A polymerases also have a 5'-3' exonuclease that is required for the removal of RNA primers from Okazaki fragments. Not all, but some Family A polymerases also a 3'-5' exonuclease that is responsible for proofreading the DNA. <ref name="structure" | In addition to the basic structure of DNA polymerase, the Family A polymerases also have a 5'-3' exonuclease that is required for the removal of RNA primers from Okazaki fragments. Not all, but some Family A polymerases also a 3'-5' exonuclease that is responsible for proofreading the DNA. <ref name="structure" /> | ||
===Family B=== | ===Family B=== | ||
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===Family X=== | ===Family X=== | ||
The thumb, palm, and fingers subdomains are a part of the of N-terminal, or 31-kDA polymerase fragment in the Family X Polymerases. The palm in this family contains three aspartic acid motifs. The fingers in this family have Helices M and N that contain amino acid residues. <ref>DOI:10.1016/j.bbapap.2009.07.008 </ref> | The thumb, palm, and fingers subdomains are a part of the of N-terminal, or 31-kDA polymerase fragment in the Family X Polymerases. The palm in this family contains three aspartic acid motifs. The fingers in this family have Helices M and N that contain amino acid residues. <ref>DOI:10.1016/j.bbapap.2009.07.008 </ref> The N-terminal is connected to an 8kDa amino terminal domain containing a 5' deoxyribose phosphate lyase that is required for base excision repair. Each member contains it's own structural differences that aid in it's functioning. <ref name="structure" /> | ||
===Family Y=== | ===Family Y=== | ||
The N-terminal of the Family Y polymerases contains the catalytic core of the fingers, palm, and thumb. The C-terminal, which has a conserved tertiary structure of a four-stranded beta sheet supported on one side by two alpha helices, otherwise referred to as the little finger domain, contributes to DNA binding and is essential for complete polymerase activity. This family lacks flexibility in the fingers subdomain, which is uncharacteristic of the other families. The other parts of the catalytic core and the little finger domain are flexible and frequently assume different positions. <ref>PMID: 20123134</ref> | The N-terminal of the Family Y polymerases contains the catalytic core of the fingers, palm, and thumb. The C-terminal, which has a conserved tertiary structure of a four-stranded beta sheet supported on one side by two alpha helices, otherwise referred to as the little finger domain, contributes to DNA binding and is essential for complete polymerase activity. This family lacks flexibility in the fingers subdomain, which is uncharacteristic of the other families. The other parts of the catalytic core and the little finger domain are flexible and frequently assume different positions. <ref>PMID: 20123134</ref> | ||
==Mechanism== | |||
The majority of DNA polymerases undergo a two-metal-ion mechanism. Two metal ions in the active site work to stabilize the pentacoordinated transition state. The first metal ion activates the hydroxyl groups. Those hydroxyl groups then go on to attack the phosphate group of the dNTP. The second metal ion not only stabilizes the negative charge, but also builds on the leaving oxygen and chelating phosphate groups. <ref name='SteitzJBiolChem1999'/> | |||
Some Dpo terminology:<br /> | Some Dpo terminology:<br /> | ||
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In the ''E. coli'', the EcDpo III subunits β, γ, δ, δ' are named '''clamp loader'''. This complex assembles the β subunit sliding clamp unto the DNA.<br /> | In the ''E. coli'', the EcDpo III subunits β, γ, δ, δ' are named '''clamp loader'''. This complex assembles the β subunit sliding clamp unto the DNA.<br /> | ||
See also [[User:Karl E. Zahn/RB69 DNA polymerase (gp43)]]<br /> | See also [[User:Karl E. Zahn/RB69 DNA polymerase (gp43)]]<br /> | ||
== 3D Structures of DNA polymerase == | |||
[[DNA polymerase 3D structures]] | |||
</StructureSection> | |||
== References == | == References == | ||
<references/> | <references/> | ||