DNA Polymerase III Holoenzyme - Wikipedia

Primary enzyme complex involved in prokaryotic DNA replication "Pol III" redirects here. For the Norwegian guard vessel from WWII, see HNoMS Pol III.

Parts of this article (those related to number of pol III enzymes and how the replication fork moves (use DNA polymerase § Pol III, PMID 28002733, 30292863)) need to be updated. Please help update this article to reflect recent events or newly available information. (December 2023)

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 corrects replication mistakes by means of exonuclease activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the replisome, which is located at the replication fork.

Components

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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.[1])
  • the α subunit (encoded by the dnaE gene) has the polymerase activity.
  • the ε subunit (dnaQ) has 3'→5' exonuclease activity.
  • the θ subunit (holE) stimulates the ε subunit's proofreading.
• 2 β units (dnaN) which act as sliding DNA clamps, they keep the polymerase bound to the DNA.
• 2 τ units (dnaX) 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 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. X can also mediate the switch from RNA primer to DNA.[2]

Activity

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DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second.[3] 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):[citation needed]

("!" for RNA, '"$" for DNA, "*" for 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

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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:[citation needed]

* * * * ! ! ! ! _ _ _ _ _ _ _ _ | DNA | <--deoxyribose (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

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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.[citation needed]

-----------> * * * * ! ! ! ! $ $ $ $ $ $ _ _ _ _ _ _ _ _ _ _ _ _ _ _| 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

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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.[citation needed]

See also

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• Beta clamp
• DNA polymerase
• DNA replication

References

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1. ^ Reyes-Lamothe R, Sherratt D, Leake M (2010). "Stoichiometry and Architecture of Active DNA Replication Machinery in Escherichia Coli". Science. 328 (5977): 498–501. Bibcode:2010Sci...328..498R. doi:10.1126/science.1185757. PMC 2859602. PMID 20413500.
2. ^ 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. doi:10.1074/jbc.270.49.29570. PMID 7494000.
3. ^ 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.

External links

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• Overview at Oregon State University
• DNA+Polymerase+III at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
• Clamping down on pathogenic bacteria – how to shut down a key DNA polymerase complex

v t e DNA replication (comparing prokaryotic to eukaryotic)
Initiation	Prokaryotic(initiation) Pre-replication complex dnaC Helicase dnaA dnaB T7 Primase dnaG Eukaryotic(preparation inG1 phase) Pre-replication complex Origin recognition complex ORC1 ORC2 ORC3 ORC4 ORC5 ORC6 Cdc6 Cdt1 Minichromosome maintenance MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 Licensing factor Autonomously replicating sequence Single-strand binding protein SSBP2 SSBP3 SSBP4 RNase H RNASEH1 RNASEH2A Helicase: HFM1 Primase: PRIM1 PRIM2 Both Origin of replication/Ori/Replicon Replication fork Lagging and leading strands Okazaki fragments Primer
Replication	Prokaryotic(elongation) DNA polymerase III holoenzyme dnaC dnaE dnaH dnaN dnaQ dnaT dnaX holA holB holC holD holE Replisome DNA ligase DNA clamp Topoisomerase DNA gyrase Prokaryotic DNA polymerase: DNA polymerase I Klenow fragment Eukaryotic(synthesis inS phase) Replication factor C RFC1 Flap endonuclease FEN1 Topoisomerase Replication protein A RPA1 Eukaryotic DNA polymerase: alpha POLA1 POLA2 PRIM1 PRIM2 delta POLD1 POLD2 POLD3 POLD4 epsilon POLE POLE2 POLE3 POLE4 DNA clamp PCNA Control of chromosome duplication Both Movement: Processivity DNA ligase
Termination	Telomere: Telomerase TERT TERC DKC1

v t e Transferases: phosphorus-containing groups (EC 2.7)
2.7.1–2.7.4:phosphotransferase/kinase(PO4)	2.7.1: OH acceptor Hexo- Gluco- Fructo- Hepatic Galacto- Phosphofructo- 1 Liver Muscle Platelet 2 Riboflavin Shikimate Thymidine ADP-thymidine NAD+ Glycerol Pantothenate Mevalonate Pyruvate Deoxycytidine PFP Diacylglycerol Phosphoinositide 3 Class I PI 3 Class II PI 3 Sphingosine Glucose-1,6-bisphosphate synthase 2.7.2: COOH acceptor Phosphoglycerate Aspartate kinase Glutamate 5-kinase 2.7.3: N acceptor Creatine 2.7.4: PO4 acceptor Phosphomevalonate Adenylate Nucleoside-diphosphate Uridylate Guanylate Thiamine-diphosphate
2.7.6: diphosphotransferase(P2O7)	Ribose-phosphate diphosphokinase Thiamine diphosphokinase
2.7.7: nucleotidyltransferase(PO4-nucleoside)	Polymerase DNA polymerase DNA-directed DNA polymerase I/A γ θ ν T7 Taq II/B α δ ε ζ Pfu III/C IV/X β λ μ TDT V/Y η ι κ RNA-directed DNA polymerase Reverse transcriptase Telomerase RNA polymerase Template-directed RNA polymerase I II III IV V ssRNAP POLRMT Primase 1 2 PrimPol RNA-dependent RNA polymerase Polyadenylation PAP PNPase Phosphorolytic3′ to 5′ exoribonuclease RNase PH PNPase Nucleotidyltransferase UTP—glucose-1-phosphate uridylyltransferase Galactose-1-phosphate uridylyltransferase Guanylyltransferase mRNA capping enzyme Other Recombinase (Integrase) Transposase
2.7.8: miscellaneous	Phosphatidyltransferases CDP-diacylglycerol—glycerol-3-phosphate 3-phosphatidyltransferase CDP-diacylglycerol—serine O-phosphatidyltransferase CDP-diacylglycerol—inositol 3-phosphatidyltransferase CDP-diacylglycerol—choline O-phosphatidyltransferase Glycosyl-1-phosphotransferase N-acetylglucosamine-1-phosphate transferase
2.7.10–2.7.13: protein kinase(PO4; protein acceptor)	2.7.10: protein-tyrosine see tyrosine kinases 2.7.11: protein-serine/threonine see serine/threonine-specific protein kinases 2.7.12: protein-dual-specificity see serine/threonine-specific protein kinases 2.7.13: protein-histidine Protein-histidine pros-kinase Protein-histidine tele-kinase Histidine kinase

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Diffusion-limited enzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadie–Hofstee diagram Hanes–Woolf plot Lineweaver–Burk plot Michaelis–Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

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