# Processivity

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In [molecular biology](/source/Molecular_biology) and [biochemistry](/source/Biochemistry), **processivity** is an [enzyme](/source/Enzyme)'s ability to [catalyze](/source/Catalyze) "consecutive reactions without releasing its [substrate](/source/Enzyme_substrate_(biology))".[1]

For example, processivity is the average number of [nucleotides](/source/Nucleotide) added by a [polymerase](/source/Polymerase) [enzyme](/source/Enzyme), such as [DNA polymerase](/source/DNA_polymerase), per association event with the template strand. Because the binding of the polymerase to the template is the rate-limiting step in [DNA synthesis](/source/DNA_synthesis)[*[citation needed](https://en.wikipedia.org/wiki/Wikipedia:Citation_needed)*], the overall rate of [DNA](/source/DNA) replication during [S phase](/source/S_phase) of the [cell cycle](/source/Cell_cycle) is dependent on the processivity of the DNA polymerases performing the replication. [DNA clamp](/source/DNA_clamp) proteins are integral components of the DNA replication machinery and serve to increase the processivity of their associated polymerases. Some polymerases add over 50,000 nucleotides to a growing DNA strand before dissociating from the template strand, giving a replication rate of up to 1,000 nucleotides per second.

## DNA binding interactions

Polymerases interact with the [phosphate](/source/Phosphate) backbone and the minor groove of the DNA, so their interactions do not depend on the specific nucleotide sequence.[2] The binding is largely mediated by [electrostatic](/source/Electrostatic) interactions between the DNA and the "thumb" and "palm" domains of the metaphorically hand-shaped DNA polymerase molecule. When the polymerase advances along the DNA sequence after adding a nucleotide, the interactions with the minor groove dissociate but those with the phosphate backbone remain more stable, allowing rapid re-binding to the minor groove at the next nucleotide.

Interactions with the DNA are also facilitated by [DNA clamp](/source/DNA_clamp) proteins, which are multimeric proteins that completely encircle the DNA, with which they associate at [replication forks](/source/Replication_fork). Their central pore is sufficiently large to admit the DNA strands and some surrounding water molecules, which allows the clamp to slide along the DNA without dissociating from it and without loosening the [protein–protein interactions](/source/Protein%E2%80%93protein_interaction) that maintain the toroid shape. When associated with a DNA clamp, DNA polymerase is dramatically more processive; without the clamp most polymerases have a processivity of only about 100 nucleotides. The interactions between the polymerase and the clamp are more persistent than those between the polymerase and the DNA. Thus, when the polymerase dissociates from the DNA, it is still bound to the clamp and can rapidly reassociate with the DNA. An example of such a DNA clamp is PCNA (proliferating cell nuclear antigen) found in *S. cervesiae*.

## Polymerase processivities

Multiple DNA polymerases have specialized roles in the DNA replication process. In *[E. coli](/source/E._coli)*, which replicates its entire [genome](/source/Genome) from a single replication fork, the polymerase [DNA Pol III](/source/Pol_III) is the enzyme primarily responsible for DNA replication and forms a replication complex with extremely high processivity. The related [DNA Pol I](/source/Pol_I) has [exonuclease](/source/Exonuclease) activity and serves to degrade the [RNA primers](/source/RNA_primer) used to initiate DNA synthesis. Pol I then synthesizes the short DNA fragments in place of the former RNA fragments. Thus Pol I is much less processive than Pol III because its primary function in DNA replication is to create many short DNA regions rather than a few very long regions.

In [eukaryotes](/source/Eukaryote), which have a much higher diversity of DNA polymerases, the low-processivity initiating enzyme is called [Pol α](/source/DNA_polymerase_alpha), and the high-processivity extension enzymes are [Pol δ](/source/DNA_polymerase_delta) and [Pol ε](/source/DNA_polymerase_epsilon). Both [prokaryotes](/source/Prokaryote) and eukaryotes must "trade" bound polymerases to make the transition from initiation to elongation. This process is called polymerase switching.[3][4]

## References

1. **[^](#cite_ref-1)** [Stryer, L.](/source/Lubert_Stryer); Berg, J. M.; Tymoczko, J. L. (2002), [*Biochemistry*](https://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=stryer.TOC) (5th ed.), New York: W. H. Freeman, [ISBN](/source/ISBN_(identifier)) [0716746840](https://en.wikipedia.org/wiki/Special:BookSources/0716746840). §[27.4.4](https://web.archive.org/web/20151019152443/http://www.ncbi.nlm.nih.gov/books/NBK22587/#A3803)

1. **[^](#cite_ref-morales_2-0)** Morales, Juan C; Kool, Eric T (1999). ["Minor Groove Interactions between Polymerase and DNA: More Essential to Replication than Watson-Crick Hydrogen Bonds?"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939743). *J Am Chem Soc*. **121** (10): 2323–2324. [doi](/source/Doi_(identifier)):[10.1021/ja983502+](https://doi.org/10.1021%2Fja983502%2B). [PMC](/source/PMC_(identifier)) [2939743](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939743). [PMID](/source/PMID_(identifier)) [20852718](https://pubmed.ncbi.nlm.nih.gov/20852718).

1. **[^](#cite_ref-tsurimoto_3-0)** Tsurimoto, Toshiki; Stillman, Bruce (1991). ["Replication Factors Required for SV40 DNA Replication in Vitro"](https://doi.org/10.1016%2FS0021-9258%2818%2952386-3). *J Biol Chem*. **266** (3): 1961–1968. [doi](/source/Doi_(identifier)):[10.1016/S0021-9258(18)52386-3](https://doi.org/10.1016%2FS0021-9258%2818%2952386-3). [PMID](/source/PMID_(identifier)) [1671046](https://pubmed.ncbi.nlm.nih.gov/1671046).

1. **[^](#cite_ref-4)** Maga, Giovanni; Stucki, Manuel; Spadari, Silvio; Hübscher, Ulrich (January 2000). "DNA polymerase switching: I. Replication factor C displaces DNA polymerase α prior to PCNA loading". *Journal of Molecular Biology*. **295** (4): 791–801. [doi](/source/Doi_(identifier)):[10.1006/jmbi.1999.3394](https://doi.org/10.1006%2Fjmbi.1999.3394). [PMID](/source/PMID_(identifier)) [10656791](https://pubmed.ncbi.nlm.nih.gov/10656791).

## Further reading

- Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). *Molecular Biology of the Gene* 5th ed. Benjamin Cummings: Cold Spring Harbor Laboratory Press.

## External links

- [https://web.archive.org/web/20060517085321/http://opbs.okstate.edu/~melcher/mg/MGW4/Mg424.html](https://web.archive.org/web/20060517085321/http://opbs.okstate.edu/~melcher/mg/MGW4/Mg424.html)

- Bedford, E; Tabor, S; Richardson, C. C. (1997). ["The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC19538). *Proceedings of the National Academy of Sciences of the United States of America*. **94** (2): 479–484. [Bibcode](/source/Bibcode_(identifier)):[1997PNAS...94..479B](https://ui.adsabs.harvard.edu/abs/1997PNAS...94..479B). [doi](/source/Doi_(identifier)):[10.1073/pnas.94.2.479](https://doi.org/10.1073%2Fpnas.94.2.479). [PMC](/source/PMC_(identifier)) [19538](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC19538). [PMID](/source/PMID_(identifier)) [9012809](https://pubmed.ncbi.nlm.nih.gov/9012809).

- Tabor, S; Richardson, C. C. (1987). ["DNA sequence analysis with a modified bacteriophage T7 DNA polymerase"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC305186). *Proceedings of the National Academy of Sciences of the United States of America*. **84** (14): 4767–4771. [Bibcode](/source/Bibcode_(identifier)):[1987PNAS...84.4767T](https://ui.adsabs.harvard.edu/abs/1987PNAS...84.4767T). [doi](/source/Doi_(identifier)):[10.1073/pnas.84.14.4767](https://doi.org/10.1073%2Fpnas.84.14.4767). [PMC](/source/PMC_(identifier)) [305186](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC305186). [PMID](/source/PMID_(identifier)) [3474623](https://pubmed.ncbi.nlm.nih.gov/3474623).

v t e DNA replication (comparing prokaryotic to eukaryotic) Initiation Prokaryotic (initiation) Pre-replication complex dnaC Helicase dnaA dnaB T7 Primase dnaG Eukaryotic (preparation in G1 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 in S 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

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