DNA Polymerase

DNA polymerase is a kind of enzyme which uses parent DNA as template to catalyze the polymerization of substrate deoxyribonucleotide to form progeny DNA. These enzymes are essential for DNA replication. This enzyme was first discovered in E. coli by Arthur komberg in 1956. It is called DNA polymerase I (polI). Thomas Kornberg (son of Arthur Kornberg) and Malcolm E. Gefter discovered DNA polymerase II in 1970. Subsequently, DNA polymerase III (pol III) was found. In prokaryotes, pol III is the primary DNA polymerase and responsible for chromosome replication.

DNA Polymerase Fig. 1 Schematic of the eukaryotic replication. (Jain R, et al, 2018)

Structure of DNA Polymerase

DNA polymerases have a highly conserved structure, which means that their overall catalytic subunits vary little among different species, and irrelevant to domain structure. Conservative structures usually indicate the important and irreplaceable functions of cells, and their maintenance provides evolutionary advantages. Its shape can be described as similar to the thumb, finger, and palm areas of right hand. Palm domain seems to play a role in the transfer of phosphoryl groups in the catalytic reaction of phosphoryl transfer. When the enzyme is active, the DNA binds to the palm. The function of the finger domain is to combine nucleoside triphosphate with template library. Thumb domain plays a potential role in DNA synthesis, transport and localization.

DNA Polymerase Fig. 2 Structure of a replicative DNA polymerase. (Hübscher U, et al, 2002)

Function of DNA Polymerase

The main function of DNA polymerase is to synthesize DNA from deoxyribonucleotide (a component of DNA). Its functions can be summed up as following.

  1. Polymerization: At the RNA-OH end of the primer, dNTP is used as the substrate, and according to the instructions on the template DNA, i.e. the pairing principle of A and T, C and G, dNTP is gradually added to the 3'- OH end of the extended DNA molecule one by one and continuously to synthesize the extended DNA. This is the main function of DNA polymerase;
  2. 3'→ 5' exonuclease activity (proofreading): The main function of this kind of enzyme activity is to recognize and remove the nucleotides at the end of the growth chain of mismatched DNA from the direction of 3'→ 5'. The main function of 3'→ 5' exonuclease activity is proofreading. When the added nucleotides are not complementary with the template and free, they will be removed by 3'→ 5' exonuclease, so as to polymerize the pairs at this position again. It is thus clear that the activity of 3'→ 5' exonuclease is very important to maintain the authenticity of DNA replication, to ensure the authenticity and accuracy of the reproduction process;
  3. 5'→ 3' exonuclease activity (removal and repair): The activity is to hydrolyze the DNA chain ahead of the DNA extension chain from the direction of 5'→ 3' (i.e. only the phosphodiester bond at the double strand of DNA is cut), mainly producing 5'- deoxynucleotides. This enzyme activity may play an important role in the repair of DNA damage.

Types of DNA Polymerases

Based on sequence homology, DNA polymerases can be classified into seven different families: A, B, C, D, X, Y and RT. DNA polymerases in prokaryotes and eukaryotes are different.

Prokaryotic Polymerase

There are two forms of prokaryotic polymerase: core polymerase and whole enzyme. Core polymerases synthesize DNA from DNA template, but they can't start synthesis alone or accurately. The whole enzyme accurately initiated the synthesis. At present, Pol I, Pol II, pol III, pol IV and Pol V are found.

Prokaryotic polymerase Family Types of DNA polymerase Function
Pol I Family A Replicative and Repair Polymerases This repair polymerase is involved in excision repair with both 3'–5' and 5'–3' exonuclease activity and processing of Okazaki fragments generated during lagging strand synthesis.
Pol II Family B Replicative and Repair Polymerases Pol II has 3'–5' exonuclease activity and participates in DNA repair
Pol III Family C Replicative Polymerases DNA polymerase III holoenzyme is the primary enzyme involved in DNA replication in E. coli .
Pol IV Family Y Replicative and Repair Polymerases It and DNA polymerase II are responsible for damage repair in the stationary phase.
Pol V Family Y Replicative and Repair Polymerases involved in SOS response and translesion synthesis DNA repair mechanisms.

Eukaryotic DNA Polymerase

There are many kinds of DNA polymerases in Eukaryotes. In recent years, as PrimPol is found, 16 kinds of DNA polymerases have been found in human.

Polymerase Family Associated activities Function
α (alpha) B Primase chromosomal replication, S-phase checkpoint, DSB repair
β (beta) X dRP & AP lyase BER, single strand break repair
γ (gamma) A 3'→5' exonuclease, dRP lyase mitochondrial replication, mitochondrial BER
δ (delta) B 3'→5' exonuclease chromosomal replication, NER, BER, MMR, DSB repair
ε (epsilon) B 3'→5' exonuclease chromosomal replication, NER, BER, MMR, DSB repair, S-phase checkpoint
ζ (zeta) B   TLS, DSB repair, ICL repair, SHM
η (eta) Y   TLS, SHM
θ (theta) A   ICL repair
κ (kappa) Y   TLS
λ (lambda) X dRP lyase DSB repair, BER?
µ (mu) X TdT DSB repair
σ (sigma) X   sister chromatid cohesion
REV1 Y TdT (for dC) TLS

DNA Polymerase Fig. 3. Human template-dependent DNA polymerases. aRapid identification of several of these DNA polymerases in a short time resulted in some confusion in nomenclature that is worth mentioning briefly. The product of the human DINB1 gene was first named Pol θ, but because that designation had already been used, the human DINB1 gene product is now designated as Pol κ. When first identified, DNA polymerase λ was found to be homologous to Pol β, so that in one instance it was designated as Pol β2, but now it has its own Greek letter designation. The S. cerevisiae X-family enzyme encoded by the POL4 gene was first considered to be the yeast equivalent of mammalian Pol β, but is now known to be more closely related to mammalian Pol λ. Finally, the products of the yeast TRF4 and human TRF4-1 genes were originally designated Pol κ. Because that name was already assigned to a different gene product, the TRF4 gene products are now called Pol σ. (Jain R, et al, 2018)

Structures of the catalytic cores of Polθ and, Polν. The proteins are shown in cartoon representation and the template–primer DNA duplexes are shown as gray sticks. (a) Polu (4X0P) and (b) Poln (4XVK) consist of the inactive exonuclease (purple), palm (cyan), fingers(yellow) and thumb (orange) domains. The nascent base pairs, formed by a template base with an incoming dNTP (in the ternary complexes of Polu) or with a primer base (in the binary complex of Poln) are shown in pink. The B-site Ca2+ ion (chelated by the phosphate groups of the incoming dNTP) is shown as a light blue sphere. Dashed lines depict unstructured regions. Insert 2 in the thumb domains of Polu (60 amino acid long) and Poln (15 amino acid long) is colored red and shown in a close up view panel under the overall structures of the proteins. Arg2254 of Polu’s insert 2 forms a hydrogen bond with an oxygen atom of the phosphate group of the 30-terminal primer base.

References

  1.  Hübscher U, Maga G, Spadari S. Eukaryotic DNA polymerases[J]. Annual review of biochemistry, 2002, 71(1): 133-163.
  2. Jain R, Aggarwal A K, Rechkoblit O. Eukaryotic DNA polymerases[J]. Current opinion in structural biology, 2018, 53: 77-87.
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