Summary: DNA polymerase III subunits tau domain IV DnaB-binding
This is the Wikipedia entry entitled "DNA polymerase III holoenzyme". More...
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DNA polymerase III holoenzyme Edit Wikipedia article
- Pol III can also refer to HNoMS Pol III, a Norwegian guard vessel from WWII
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 Malcolm Gefter in 1970. The complex has high processivity (i.e. the number of nucleotides added per binding event) and, specifically referring to the replication of the E.coli genome, works in conjunction with four other DNA polymerases (Pol I, Pol II, Pol IV, and Pol V). Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that correct replication mistakes by means of exonuclease activity working 3'→5'. DNA Pol III is a component of the replisome, which is located at the replication fork.
The replisome is composed of the following:
- 2 DNA Pol III enzymes, each comprising α, ε and θ subunits.
- 2 β units (dnaN) which act as sliding DNA clamps, they keep the polymerase bound to the DNA.
- 2 τ units (dnaX) which acts 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 fragments, 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), and 1 δ' subunit (holB). The δ is involved in copying of the lagging strand.
- Χ (holC) and Ψ (holD) which form a 1:1 complex and bind to γ or τ.
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, complementary to part of the single-stranded DNA, is synthesized by primase (an RNA polymerase):
--------> * * * * ! ! ! ! _ _ _ _ _ _ _ _ | RNA | <--ribose (sugar)-phosphate backbone G U A U | Pol | <--RNA primer * * * * |_ _ _ _| <--hydrogen bonding C A T A G C A T C C <--template ssDNA (single-stranded DNA) _ _ _ _ _ _ _ _ _ _ <--deoxyribose (sugar)-phosphate backbone $ $ $ $ $ $ $ $ $ $
 Addition onto 3'OH
As replication progresses and the replisome moves forward, DNA polymerase III arrives at the RNA primer and begins replicating the DNA, adding onto the 3'OH of the primer:
* * * * ! ! ! ! _ _ _ _ _ _ _ _ | DNA | <--ribose (sugar)-phosphate backbone G U A U | Pol | <--RNA primer * * * * |_III_ _| <--hydrogen bonding C A T A G C A T C C <--template ssDNA (single-stranded DNA) _ _ _ _ _ _ _ _ _ _ <--deoxyribose (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) 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 (sugar)-phosphate backbone G U A U C G T A G G| Pol | <--RNA primer * * * * * * * * * *|_III_ _| <--hydrogen bonding C A T A G C A T C C <--template ssDNA (single-stranded DNA) _ _ _ _ _ _ _ _ _ _ <--deoxyribose (sugar)-phosphate backbone $ $ $ $ $ $ $ $ $ $
 Removal of primer
After replication of the desired region, the RNA primer is removed by DNA polymerase I via the process of nick translation. The removal of the RNA primer allows DNA ligase 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
- DNA replication
- DNA polymerase
- Beta clamp
- Clamping down on pathogenic bacteria – how to shut down a key DNA polymerase complex
- Olson MW, Dallmann HG, McHenry CS (December 1995). "DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' to a physiologically relevant range". J. Biol. Chem. 270 (49): 29570–7. PMID 7494000.
- Kelman Z, O'Donnell M (1995). "DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine". Annu. Rev. Biochem. 64: 171–200. doi:10.1146/annurev.bi.64.070195.001131. PMID 7574479.
- Overview at Oregon State University
- DNA Polymerase III at the US National Library of Medicine Medical Subject Headings (MeSH)
DNA polymerase III subunits tau domain IV DnaB-binding Provide feedback
This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau.
Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE;, Nucleic Acids Res. 2007;35:2813-2824.: The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. PUBMED:17355988 EPMC:17355988
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR022001
This domain found in bacterial proteins, and is approximately 80 amino acids in length. It is found in association with . domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding domain IV and all of the alpha-interacting domain V are unique to tau.
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Curation and family details
|Seed source:||PFAM-B_2296 (release 23.0)|
|Author:||Assefa S, Bateman A, Coggill P|
|Number in seed:||16|
|Number in full:||635|
|Average length of the domain:||82.10 aa|
|Average identity of full alignment:||63 %|
|Average coverage of the sequence by the domain:||13.02 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||3|
|Download:||download the raw HMM for this family|
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