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DNA polymerase II – Definition, Structure, Mechanism, Functions

Sourav Bio

What is DNA polymerase II?

  • DNA polymerase II (DNA Pol II), also referred to as Pol II, is a DNA-dependent DNA polymerase found in prokaryotic organisms. Encoded by the PolB gene, DNA Pol II plays a crucial role in DNA replication and repair processes within these microorganisms.
  • With a molecular mass of approximately 89.9 kilodaltons (kDa), DNA Pol II belongs to the B family of DNA polymerases. Its discovery and initial characterization can be attributed to the work of Thomas Kornberg in 1970, followed by further elucidation in subsequent years. While the precise in vivo functionality of DNA Pol II remains a subject of debate, a consensus has emerged indicating that it predominantly serves as a backup enzyme in prokaryotic DNA replication.
  • DNA Pol II exhibits DNA synthesis capabilities in the 5′ to 3′ direction, a fundamental attribute for DNA polymerases. Additionally, it possesses 3′ to 5′ exonuclease proofreading activity, ensuring the fidelity of DNA replication. To augment its performance and accuracy, DNA Pol II interacts with several binding partners shared with DNA Pol III.
  • The historical context of DNA polymerases in Escherichia coli (E. coli) sheds light on the emergence of DNA Pol II. Initially, DNA polymerase I (DNA Pol I) was the first DNA-directed DNA polymerase isolated from E. coli. Early investigations suggested that DNA Pol I primarily participated in repair replication rather than being the main replicative polymerase. The creation of E. coli mutants deficient in DNA Pol I, termed Pol A1− mutants, in 1969 by De Lucia and Cairns provided further insights. These mutants exhibited increased sensitivity to ultraviolet light, supporting the notion that DNA Pol I was involved in repair replication. However, the mutants grew at a normal rate, indicating the presence of an alternative enzyme responsible for DNA replication.
  • This pivotal discovery led to the isolation and characterization of DNA Pol II, which was initially believed to be the principal replicative enzyme in E. coli. The crystallization of DNA Pol II by Anderson and colleagues in 1994 marked a significant milestone in understanding its structural properties.
  • In more recent developments, research conducted in 2023 highlighted the connection between accelerated transcription associated with aging and an increased error rate in DNA replication mediated by Pol II. This heightened error rate can result in the production of flawed DNA copies, potentially contributing to the onset of various diseases.
  • In summary, DNA polymerase II, encoded by the PolB gene, is a prokaryotic DNA-dependent DNA polymerase belonging to the B family of DNA polymerases. While its exact in vivo role continues to be debated, DNA Pol II is recognized as a backup enzyme in prokaryotic DNA replication, possessing both DNA synthesis and proofreading capabilities. Its historical significance in E. coli research and recent implications in aging-related disease underscore its importance in molecular biology and genetics.

Definition of DNA polymerase II

DNA polymerase II (DNA Pol II) is a prokaryotic DNA-dependent DNA polymerase that primarily functions as a backup enzyme in DNA replication and repair processes. It belongs to the B family of DNA polymerases and possesses DNA synthesis and proofreading activities.

Structure of DNA polymerase II

  • The structure of DNA polymerase II (DNA Pol II) is a subject of scientific interest due to its role in DNA replication and repair processes in prokaryotic organisms. DNA Pol II is an 89.9-kilodalton (kD) protein, composed of a linear sequence of 783 amino acids, and is encoded by the polB (dinA) gene.
  • Unlike some other polymerases that form complexes, DNA Pol II functions as a monomeric enzyme. Its monomeric structure comprises three distinct regions, often colloquially referred to as the “palm,” “fingers,” and “thumb.” These structural components collectively resemble a “hand” that envelops a single strand of DNA during the polymerization process.
  • The “palm” region of DNA Pol II is of particular importance, as it houses three catalytic residues critical for its enzymatic activity. These residues coordinate with two divalent metal ions to facilitate DNA synthesis. This metal-ion coordination is essential for the accurate and efficient addition of nucleotides to the growing DNA strand.
  • One noteworthy feature of DNA Pol II is its relatively high abundance within the cell. Prokaryotic cells typically contain a substantial number of DNA Pol II copies, estimated to range between 30 to 50 molecules. In contrast, DNA Pol III, another DNA polymerase involved in replication, is present in significantly fewer copies, approximately five times less than DNA Pol II.
  • In terms of structural classification, DNA Pol II belongs to Group B of DNA polymerases, a categorization based on similarities in both structure and function. This group includes several homologs, such as human DNA Pol α, δ, ϵ, and ζ, as well as other DNA polymerases like RB69, 9°N-7, and Tgo. Notably, DNA Pol II distinguishes itself from other members of Group B by functioning as a monomeric enzyme, whereas many of its counterparts have at least one additional subunit.
  • In summary, DNA polymerase II (DNA Pol II) exhibits a well-defined structural organization, with its monomeric configuration featuring distinct “palm,” “fingers,” and “thumb” regions. The catalytic activity of DNA Pol II is centered in its palm region, where key residues facilitate nucleotide addition during DNA synthesis. Its classification within Group B polymerases underscores its evolutionary relationship with other DNA polymerases, although its monomeric nature sets it apart within this category. Understanding the structure of DNA Pol II is essential for comprehending its functional role in DNA replication and repair in prokaryotic cells.

Mechanism of DNA polymerase II

The mechanism of DNA polymerase II (DNA Pol II) is a finely orchestrated process that ensures the accurate repair of damaged DNA sequences and the maintenance of genomic integrity during DNA replication. This mechanism involves several critical steps and molecular interactions:

  1. Recognition of Damaged DNA: During DNA replication, the sequence of base pairs can be compromised by various forms of damage, leading to the stalling of replication. DNA Pol II plays a pivotal role in repairing these errors. In vitro studies have shown that DNA Pol II occasionally interacts with proteins associated with DNA Pol III, such as the β-clamp and clamp loading complex. This interaction allows DNA Pol II access to the nascent strand of DNA. This strategic placement of DNA Pol II makes sense, as any errors introduced by DNA Pol III occur on the nascent strand, rather than the conservative strand.
  2. N-Terminal Domain Interaction: The N-terminal domain of DNA Pol II is responsible for the association and dissociation of the DNA strand with the catalytic subunit of the enzyme. Within the N-terminal domain, there are likely two distinct sites that recognize single-stranded DNA. One site is responsible for recruiting single-stranded DNA to DNA Pol II, while another site is responsible for the dissociation of single-stranded DNA from DNA Pol II. These interactions are critical for the enzyme’s function in repairing damaged DNA.
  3. Catalytic Activity: Upon binding to its substrate, DNA Pol II engages in the binding of nucleoside triphosphates, which helps maintain the hydrogen-bonded structure of DNA. The enzyme accurately selects the correct deoxyribonucleoside triphosphate (dNTP) complementary to the template strand. This selection is crucial for maintaining the fidelity of DNA repair. During this process, the enzyme undergoes conformational changes in its subdomains and amino acid residues, facilitating rapid repair synthesis.
  4. Active Site and Catalysis: The active site of DNA Pol II plays a central role in catalyzing the repair of damaged DNA. This active site contains two magnesium ions, which are crucial for stabilizing the catalytic Aspartic Acids D419 and D547. Magnesium ions also play a role in coordinating conformational changes in active site amino acid residues. These conformational changes are essential for the catalytic activity of DNA Pol II. Initially, magnesium ions bind to the DNA and dNTP in the open state, enabling the necessary conformational changes. After catalysis, magnesium ions are released, and the enzyme returns to its open state, ready for subsequent repair events.

In summary, DNA polymerase II operates through a well-coordinated mechanism that involves the recognition of damaged DNA, interaction with the nascent DNA strand, accurate selection of dNTPs, and catalysis at its active site. These precise molecular interactions ensure the fidelity of DNA repair, making DNA Pol II a crucial enzyme in safeguarding genomic stability during DNA replication and damage repair processes.

Species distribution of DNA polymerase II

The distribution and role of DNA polymerase II (Pol II) vary between prokaryotic and eukaryotic organisms, reflecting its significance in DNA replication and repair in different biological contexts.

Prokaryotic Distribution

In prokaryotic organisms, Pol II is a member of the polymerase B family and plays a crucial role in safeguarding the fidelity of DNA replication. Specifically:

  1. Supporting Pol III in DNA Replication: Pol II collaborates with the primary replicative polymerase, Pol III, during DNA replication, where the replication machinery moves along the DNA strand from the 3′ end to the 5′ end. While Pol III is highly efficient, it occasionally stalls during replication errors, potentially leading to the misincorporation of nucleotides.
  2. Proofreading and Error Correction: Pol II’s primary function is to serve as a backup error-correcting enzyme. It has a significantly higher fidelity factor compared to Pol III, which means it is less prone to creating mispairings. When Pol III encounters a mismatched base, Pol II can interrupt the replication process, excise the mismatched bases, and replace them with the correct ones. This proofreading function ensures the accuracy of DNA replication and prevents the accumulation of mutations.
  3. Protection Against Mutations: Pol II also acts as a barrier against mutations caused by the more error-prone Pol IV. Pol IV is capable of repairing mismatched base pairings starting from the 3′ end of the DNA strand. In the presence of Pol II, it is blocked from acting on the 3′ end. This protective function of Pol II prevents the formation of mutations while it functions normally. If Pol II is impaired or incapacitated due to mutations or other factors, Pol IV can step in to correct the mispaired bases, albeit with a higher error rate.

Eukaryotic Distribution

In eukaryotic organisms, Pol II does not naturally participate in the DNA replication process alongside the eukaryotic members of the polymerase B family. However, it shares structural and functional motifs with these polymerases. The polymerases in this family include Pol α, ε, ζ, and δ. These polymerases predominantly proofread the newly synthesized DNA in the 3’→5′ direction and can synthesize DNA on both the leading and lagging strands during replication. They are characterized by their high accuracy, which allows them to rectify mispairings that may occur during DNA synthesis.

In summary, the distribution of DNA polymerase II varies between prokaryotic and eukaryotic organisms, reflecting its distinct roles in maintaining DNA replication fidelity and preventing mutations. In prokaryotes, Pol II acts as a backup polymerase to correct errors during replication and protect against mutations, while in eukaryotes, it shares functional similarities with other polymerases in the same family, collectively contributing to the precision of DNA synthesis.

Functions of DNA polymerase II

DNA polymerase II (DNA Pol II) is a multifaceted prokaryotic enzyme with several distinct functions, contributing to various aspects of DNA maintenance and cellular survival. While not the primary polymerase involved in chromosome replication in prokaryotes like E. coli, DNA Pol II performs crucial roles in DNA replication, repair, and maintaining genomic integrity.

  1. DNA Replication: DNA replication is a fundamental process in cell proliferation, enabling the transmission of genetic information to progeny. Although DNA Pol III is the primary replicative polymerase in prokaryotes like E. coli due to its speed and efficiency, DNA Pol II also participates in DNA replication. DNA Pol II’s comparatively slower pace is compensated by its remarkable accuracy. It possesses 3′→5′ exonuclease activity and primase activity, allowing it to proofread and correct errors introduced by other polymerases, such as Pol III. Moreover, DNA Pol II exhibits high fidelity, with a low substitution error rate (≤ 2×10^−6) and an even lower −1 frameshift error rate (≤ 1×10^−6). DNA Pol II is particularly involved in replicating the lagging strand during DNA replication and can be specifically recruited when Pol III encounters obstacles or stalls, ensuring the continuity of DNA synthesis.
  2. DNA Repair: DNA is susceptible to various forms of damage, including UV irradiation and chemical agents like nitrogen mustard and psoralen, which induce inter-strand cross-links. DNA Pol II plays a pivotal role in repairing these inter-strand cross-links, a challenging task as both DNA strands are damaged, resulting in incorrect genetic information on both strands. Although the exact mechanism of repair is still under investigation, DNA Pol II’s high involvement in this process underscores its significance in maintaining DNA integrity.
  3. Other Proposed Functions: While DNA Pol II’s primary functions in replication and repair are well-established, there are other proposed functions that remain to be fully confirmed. These include its potential involvement in repairing UV-damaged DNA, aiding in replication restart in UV-irradiated E. coli, contributing to adaptive mutagenesis, and possibly playing a role in long-term survival under certain conditions. Further research is required to conclusively validate these proposed functions.

In summary, DNA polymerase II, despite not being the primary replicative polymerase in prokaryotes, serves vital roles in DNA replication and repair processes. Its accuracy, proofreading capabilities, and involvement in repairing inter-strand cross-links highlight its importance in maintaining genomic stability and ensuring the faithful transmission of genetic information. Ongoing research continues to uncover additional functions and nuances of this versatile enzyme.


What is the primary function of DNA polymerase II (Pol II) in prokaryotic organisms?
a) Leading strand DNA replication
b) Lagging strand DNA replication
c) Proofreading during DNA replication
d) Repairing DNA damage

Which gene encodes DNA polymerase II in prokaryotes?
a) polA
b) polB
c) polC
d) polD

In the prokaryotic DNA replication process, which polymerase is primarily responsible for replicating the lagging strand?
a) DNA Pol I
b) DNA Pol III
c) DNA Pol II
d) DNA Pol IV

DNA Pol II is known for its high fidelity during DNA replication. What does this mean?
a) It replicates DNA rapidly.
b) It can repair DNA damage quickly.
c) It is less likely to introduce errors in DNA synthesis.
d) It synthesizes both DNA strands simultaneously.

Which type of mutation can DNA Pol II help prevent during DNA replication?
a) Point mutations
b) Silent mutations
c) Frameshift mutations
d) Transversion mutations

What is the role of DNA Pol II in protecting against mutations caused by DNA Pol IV?
a) It promotes Pol IV activity.
b) It competes with Pol IV for binding to DNA.
c) It has no effect on Pol IV.
d) It enhances Pol III function.

In eukaryotic organisms, which DNA polymerase family does DNA Pol II belong to?
a) Polymerase A family
b) Polymerase B family
c) Polymerase C family
d) Polymerase D family

Which direction does DNA Pol II primarily proofread during DNA synthesis in eukaryotes?
a) 5’→3′
b) 3’→5′
c) 3’→5′ on both strands
d) 5’→3′ on both strands

What is the primary function of DNA polymerases in the polymerase B family in eukaryotes?
a) Leading strand DNA replication
b) Repair of inter-strand cross-links
c) Proofreading during RNA synthesis
d) Removal of mismatched bases

Which characteristic distinguishes DNA Pol II from other DNA polymerases in the B family in eukaryotes?
a) High error rate
b) Leading strand synthesis
c) Proofreading in the 5’→3′ direction
d) Synthesis on both leading and lagging strands


What is DNA polymerase II (Pol II)?

DNA polymerase II, often abbreviated as Pol II, is an enzyme involved in DNA replication and repair processes in prokaryotic organisms.

What is the primary function of DNA polymerase II?

The primary function of DNA polymerase II is to repair DNA damage and correct errors in DNA replication to maintain genomic integrity.

Which gene encodes DNA polymerase II in prokaryotes?

DNA polymerase II is encoded by the polB (dinA) gene in prokaryotic organisms.

How does DNA polymerase II differ from DNA polymerase III in prokaryotic DNA replication?

DNA polymerase III is the primary replicative polymerase in prokaryotes, while DNA polymerase II serves as a backup enzyme. Pol II’s high fidelity helps correct errors made by Pol III.

What is the proofreading capability of DNA polymerase II?

DNA polymerase II has a high proofreading capability, meaning it can recognize and correct errors in the newly synthesized DNA strand during replication.

How does DNA polymerase II protect against mutations caused by DNA polymerase IV (Pol IV)?

DNA polymerase II competes with DNA polymerase IV for binding to DNA, preventing Pol IV from acting and introducing mutations.

Does DNA polymerase II have a role in eukaryotic DNA replication?

While DNA polymerase II primarily functions in prokaryotes, it shares structural and functional similarities with other polymerases in the B family in eukaryotes, contributing to DNA synthesis accuracy.

What type of mutations can DNA polymerase II help prevent during DNA replication?

DNA polymerase II helps prevent frameshift mutations, which involve the insertion or deletion of bases, by correcting errors in DNA synthesis.

Is DNA polymerase II involved in repairing specific types of DNA damage?

Yes, DNA polymerase II is particularly involved in repairing inter-strand cross-links, which are cytotoxic lesions caused by chemical agents.

What is the significance of DNA polymerase II’s proofreading activity in DNA replication?

DNA polymerase II’s proofreading activity ensures that errors introduced during DNA replication are corrected promptly, maintaining the accuracy of the genetic code and preventing the accumulation of mutations.

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