# DNA polymerase III holoenzyme
**DNA polymerase III holoenzyme** (Pol III HE) is the multisubunit enzyme that performs most replicative DNA synthesis in *Escherichia coli*. It contains two DNA polymerases embedded in a particle with 9 other subunits, 10 distinct subunits in total, organized into a catalytic core, a ring-shaped sliding clamp, and an ATP-dependent clamp loader[1](https://www.annualreviews.org/content/journals/10.1146/annurev.bi.64.070195.001131) • [2](https://pmc.ncbi.nlm.nih.gov/articles/PMC4238392/). In overall structure and function it resembles the chromosomal replicases of eukaryotes, from yeast to humans[1](https://www.annualreviews.org/content/journals/10.1146/annurev.bi.64.070195.001131).
| Key fact | Detail |
|---|---|
| Role | The chromosomal replicase of *E. coli*, responsible for most replicative synthesis[1](https://www.annualreviews.org/content/journals/10.1146/annurev.bi.64.070195.001131) • [3](https://www.sciencedirect.com/science/article/pii/S1874604708603297) |
| Composition | 10 distinct subunits in three functional parts: the αεθ core, the β sliding clamp, and the five-protein γ complex clamp loader[2](https://pmc.ncbi.nlm.nih.gov/articles/PMC4238392/) • [4](https://odonnell.rockefeller.edu/assets/pdfs/79.pdf) |
| Core subunits | α (130 kD, dnaE gene) carries polymerase activity; ε (27 kD, dnaQ/mutD) carries 3′→5′ proofreading exonuclease activity; θ (9 kD, holE) is a small subunit[2](https://pmc.ncbi.nlm.nih.gov/articles/PMC4238392/) |
| Sliding clamp | The β subunit is a dimer shaped as a ring with a central cavity that encircles duplex DNA, tethering the polymerase to the template[5](https://www.sciencedirect.com/science/article/pii/S0021925818922866) |
| Clamp loader | The γ complex (γδδ′χψ) couples ATP hydrolysis to assembly of β clamps around primed DNA[4](https://odonnell.rockefeller.edu/assets/pdfs/79.pdf) |
| Dimeric architecture | The τ subunit dimerizes the two Pol III cores, allowing simultaneous copying of leading and lagging strands[6](https://pmc.ncbi.nlm.nih.gov/articles/PMC3391330/) |
| Fidelity | *E. coli* chromosomal replication has an error rate of 10−9 to 10−11 errors per base pair[7](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1574-6976.2012.00338.x) |
## Discovery and nomenclature
DNA polymerase III was detected in 1971 during the purification of *E. coli* polymerase II, and the dnaE gene encoding its catalytic α subunit was sequenced in 1987[8](https://www.nichd.nih.gov/research/atNICHD/Investigators/woodgate/research/DNA-polymerases). The holoenzyme form, the more complex physiological form of Pol III, was isolated using an assay based on in vitro replication of natural chromosomes[3](https://www.sciencedirect.com/science/article/pii/S1874604708603297). Once all 10 subunits had been purified individually or as complexes, they could be reconstituted to generate a polymerase with the high catalytic rate of the intact holoenzyme[9](https://www.sciencedirect.com/science/article/pii/S0021925818686788).
## The polymerase core
The Pol III core consists of three subunits. The 130 kD α subunit, encoded by dnaE, carries the polymerase activity. The 27 kD ε subunit, encoded by dnaQ (also called mutD), carries the 3′→5′ exonuclease that removes mispaired nucleotides, and the 9 kD θ subunit is encoded by holE[2](https://pmc.ncbi.nlm.nih.gov/articles/PMC4238392/). Unlike polymerases I and II, where proofreading resides in a domain of the polymerase polypeptide itself, Pol III places its exonuclease on a separate subunit[2](https://pmc.ncbi.nlm.nih.gov/articles/PMC4238392/) • [10](https://pmc.ncbi.nlm.nih.gov/articles/PMC6153641/).
**Proofreading specificity.** The ε subunit hydrolyzes mispaired nucleotides at a higher rate than correctly paired ones, whether isolated or integrated into the core or holoenzyme[11](https://pmc.ncbi.nlm.nih.gov/articles/PMC1134117/). This specificity is thought to arise from melting of the DNA 3′ terminus, which occurs more readily at a mispair than at a matched pair; the physiologically relevant substrate for ε within the holoenzyme is probably single-stranded DNA of at least three nucleotides[11](https://pmc.ncbi.nlm.nih.gov/articles/PMC1134117/). Proofreading raises the overall fidelity of DNA synthesis by a factor of 102 to 103, depending on the polymerase and the mispair[10](https://pmc.ncbi.nlm.nih.gov/articles/PMC6153641/).
## The β sliding clamp
The β subunit is a dimer in the shape of a ring with a central cavity large enough to encircle duplex DNA[5](https://www.sciencedirect.com/science/article/pii/S0021925818922866). Once loaded, the ring slides along DNA and clamps the rest of the machinery to the template, conferring the high processivity needed to copy long stretches without dissociating[1](https://www.annualreviews.org/content/journals/10.1146/annurev.bi.64.070195.001131). β binds the polymerase directly through contact with the α subunit[12](https://cmgm-new.stanford.edu/biochem/biochem201/Papers/odonnell.pdf).
## The γ complex clamp loader
Sliding clamps cannot assemble around DNA by themselves, so the holoenzyme includes a five-protein clamp loader, the γ complex (γδδ′χψ), which couples ATP hydrolysis to placement of β rings around primed DNA[4](https://odonnell.rockefeller.edu/assets/pdfs/79.pdf). The detailed mechanism has been worked out as follows. ATP is not needed to crack open the β ring; its function is to regulate the δ subunit, which opens the clamp simply by binding to it. On ATP binding, the δ′ subunit, a modulator of the δ–β interaction, permits δ to bind β and split the ring at one interface. The loader-open clamp complex then encounters primed DNA, and DNA binding stimulates ATP hydrolysis, which ejects the γ complex and leaves the ring to close around the duplex[13](https://pubmed.ncbi.nlm.nih.gov/9927437/).
The χ subunit of the clamp loader contacts single-stranded DNA-binding protein (SSB) to promote processive elongation and sliding clamp assembly[4](https://odonnell.rockefeller.edu/assets/pdfs/79.pdf).
## A two-polymerase machine at the fork
The τ subunit dimerizes the two Pol III cores within the holoenzyme, creating a dimeric polymerase capable of copying the two DNA strands simultaneously[6](https://pmc.ncbi.nlm.nih.gov/articles/PMC3391330/) • [5](https://www.sciencedirect.com/science/article/pii/S0021925818922866). τ also interacts with the DnaB helicase and in this way regulates the speed of the replication fork, and it controls lagging-strand cycling by mediating release of the Pol III core from its β clamp upon completion of each Okazaki fragment[6](https://pmc.ncbi.nlm.nih.gov/articles/PMC3391330/).
Replication of the whole *E. coli* genome, 4700 kb, proceeds continuously from the origin to the terminus, with the replication fork marking the moving point of synthesis[14](https://lib.ysu.am/open_books/311870_1.pdf).
## Fidelity and accessory polymerases
The error rate of *E. coli* chromosomal replication is as low as 10−9 to 10−11 errors per base pair[7](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1574-6976.2012.00338.x). Genetic analysis of mutation rates shows that this accuracy is a multi-polymerase affair: Pol II serves as a back-up proofreader for Pol III, processing mispairs created during chromosomal replication, while Pols IV and V do not normally contribute significantly to fidelity but can do so under elevated expression, in a lagging-strand-specific manner. Pol I contributes a lagging-strand-specific fidelity role limited to faithful filling of Okazaki fragment gaps[7](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1574-6976.2012.00338.x). The τ subunit also has a fidelity role, controlling access of these accessory polymerases to the fork[6](https://pmc.ncbi.nlm.nih.gov/articles/PMC3391330/).
## Comparison with eukaryotic replicases
Cellular replicases from prokaryotes to eukaryotes share the same three-component design: a [DNA polymerase](https://www.edgepedia.org/dna-polymerase), a ring-shaped sliding clamp, and a clamp loader[15](https://www.sciencedirect.com/science/article/pii/S0960982201005590). The *E. coli* holoenzyme is very similar in structure and function to the chromosomal replicases of eukaryotes from yeast to humans[1](https://www.annualreviews.org/content/journals/10.1146/annurev.bi.64.070195.001131); the eukaryotic counterpart of the β clamp is PCNA, and the eukaryotic clamp loader is RFC, whose architecture the γ complex structural findings were used to predict[15](https://www.sciencedirect.com/science/article/pii/S0960982201005590).
## References
1. [Kelman, Z. and O'Donnell, M. (1995). DNA Polymerase III Holoenzyme: Structure and Function of a Chromosomal Replicating Machine. Annual Review of Biochemistry 64:171-200.](https://www.annualreviews.org/content/journals/10.1146/annurev.bi.64.070195.001131)
2. [The DNA exonucleases of Escherichia coli, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4238392/)
3. [DNA Polymerase III Holoenzyme, The Enzymes Volume 14 (1981), ScienceDirect](https://www.sciencedirect.com/science/article/pii/S1874604708603297)
4. [Devoted to the lagging strand: the χ subunit of DNA polymerase III holoenzyme contacts SSB, O'Donnell lab](https://odonnell.rockefeller.edu/assets/pdfs/79.pdf)
5. [Assembly of a Chromosomal Replication Machine: Two DNA Polymerases, a Clamp Loader, and Sliding Clamps in One Holoenzyme Particle, J Biol Chem](https://www.sciencedirect.com/science/article/pii/S0021925818922866)
6. [DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC3391330/)
7. [Fijalkowska, Schaaper and Jonczyk (2012). DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair. FEMS Microbiology Reviews 36:1105-1121.](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1574-6976.2012.00338.x)
8. [DNA polymerases, 60 years of discoveries, Roger Woodgate Lab, NICHD](https://www.nichd.nih.gov/research/atNICHD/Investigators/woodgate/research/DNA-polymerases)
9. [DNA polymerase III holoenzyme of Escherichia coli. III. Distinctive processive polymerases reconstituted from purified subunits, J Biol Chem](https://www.sciencedirect.com/science/article/pii/S0021925818686788)
10. [Fidelity of DNA replication: a matter of proofreading, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6153641/)
11. [Dysfunctional proofreading in the Escherichia coli DNA polymerase III core, PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC1134117/)
12. [Mechanism of the Sliding β-Clamp of DNA Polymerase III Holoenzyme, O'Donnell](https://cmgm-new.stanford.edu/biochem/biochem201/Papers/odonnell.pdf)
13. [Turner, Hingorani, Kelman and O'Donnell (1999). The internal workings of a DNA polymerase clamp-loading machine. EMBO J 18:771-783.](https://pubmed.ncbi.nlm.nih.gov/9927437/)
14. [DNA polymerase III holoenzyme (Encyclopedia reference), PDF](https://lib.ysu.am/open_books/311870_1.pdf)
15. [Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC, Current Biology](https://www.sciencedirect.com/science/article/pii/S0960982201005590)
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*Topic: Encyclopedia › Life and health › Biological foundations › Biochemistry and metabolism › Enzyme classes and activities › DNA and RNA processing enzyme activities › Nucleic-acid polymerases › Families C and D DNA polymerases*
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