Polymerase

Short description: Class of enzymes which synthesize nucleic acid chains or polymers

Structure of Taq DNA polymerase

In biochemistry, a polymerase is an enzyme (EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base-pairing interactions or RNA by half ladder replication.

A DNA polymerase from the thermophilic bacterium, Thermus aquaticus (Taq) (PDB 1BGX, EC 2.7.7.7) is used in the polymerase chain reaction, an important technique of molecular biology.

A polymerase may be template-dependent or template-independent. Poly-A-polymerase is an example of template independent polymerase. Terminal deoxynucleotidyl transferase also known to have template independent and template dependent activities.

Types

By function

Classes of Template dependent polymerase
	DNA-polymerase	RNA-polymerase
Template is DNA	DNA dependent DNA-polymerase or common DNA polymerases	DNA dependent RNA-polymerase or common RNA polymerases
Template is RNA	RNA dependent DNA polymerase or Reverse transcriptase	RNA dependent RNA polymerase or RdRp or RNA-replicase

DNA polymerase (DNA-directed DNA polymerase, DdDP)
- Family A: DNA polymerase I; Pol γ, θ, ν
- Family B: DNA polymerase II; Pol α, δ, ε, ζ
- Family C: DNA polymerase III holoenzyme
- Family X: Pol β, λ, μ
  - Terminal deoxynucleotidyl transferase (TDT), which lends diversity to antibody heavy chains.^[1]
- Family Y: DNA polymerase IV (DinB) and DNA polymerase V (UmuD'2C) - SOS repair polymerases; Pol η, ι, κ
Reverse transcriptase (RT; RNA-directed DNA polymerase; RdDP)
- Telomerase
DNA-directed RNA polymerase (DdRP, RNAP)
- Multi-subunit (msDdRP): RNA polymerase I, RNA polymerase II, RNA polymerase III
- Single-subunit (ssDdRP): T7 RNA polymerase, POLRMT
- Primase, PrimPol
RNA replicase (RNA-directed RNA polymerase, RdRP)
- Viral (single-subunit)
- Eukaryotic cellular (cRdRP; dual-subunit)
Template-less RNA elongation
- Polyadenylation: PAP, PNPase

By structure

Polymerases are generally split into two superfamilies, the "right hand" fold (InterPro: IPR043502) and the "double psi beta barrel" (often simply "double-barrel") fold. The former is seen in almost all DNA polymerases and almost all viral single-subunit polymerases; they are marked by a conserved "palm" domain.^[2] The latter is seen in all multi-subunit RNA polymerases, in cRdRP, and in "family D" DNA polymerases found in archaea.^[3]^[4] The "X" family represented by DNA polymerase beta has only a vague "palm" shape, and is sometimes considered a different superfamily (InterPro: IPR043519).^[5]

Primases generally don't fall into either category. Bacterial primases usually have the Toprim domain, and are related to topoisomerases and mitochondrial helicase twinkle.^[6] Archae and eukaryotic primases form an unrelated AEP family, possibly related to the polymerase palm. Both families nevertheless associate to the same set of helicases.^[7]

Right hand structure of Bacteriophage RB69, a family B DdRP.

References

↑ "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination". Structure 24 (9): 1452–63. September 2016. doi:10.1016/j.str.2016.06.014. PMID 27499438.
↑ "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure 5 (8): 1109–22. August 1997. doi:10.1016/S0969-2126(97)00261-X. PMID 9309225.
↑ "Multisubunit RNA polymerases". Current Opinion in Structural Biology 12 (1): 89–97. February 2002. doi:10.1016/S0959-440X(02)00294-4. PMID 11839495.
↑ "The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution". Journal of Molecular Biology 431 (20): 4167–4183. September 2019. doi:10.1016/j.jmb.2019.05.017. PMID 31103775.
↑ "The structure of an RNAi polymerase links RNA silencing and transcription". PLoS Biology 4 (12): e434. December 2006. doi:10.1371/journal.pbio.0040434. PMID 17147473.
↑ "Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins". Nucleic Acids Research 26 (18): 4205–13. September 1998. doi:10.1093/nar/26.18.4205. PMID 9722641.
↑ "Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members". Nucleic Acids Research 33 (12): 3875–96. 2005. doi:10.1093/nar/gki702. PMID 16027112.

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[1] "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination". Structure 24 (9): 1452–63. September 2016. doi:10.1016/j.str.2016.06.014. PMID 27499438.

[pmid9309225-2] "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure 5 (8): 1109–22. August 1997. doi:10.1016/S0969-2126(97)00261-X. PMID 9309225.

[pmid11839495-3] "Multisubunit RNA polymerases". Current Opinion in Structural Biology 12 (1): 89–97. February 2002. doi:10.1016/S0959-440X(02)00294-4. PMID 11839495.

[qde1-mono-4] "The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution". Journal of Molecular Biology 431 (20): 4167–4183. September 2019. doi:10.1016/j.jmb.2019.05.017. PMID 31103775.

[5] "The structure of an RNAi polymerase links RNA silencing and transcription". PLoS Biology 4 (12): e434. December 2006. doi:10.1371/journal.pbio.0040434. PMID 17147473.

[6] "Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins". Nucleic Acids Research 26 (18): 4205–13. September 1998. doi:10.1093/nar/26.18.4205. PMID 9722641.

[7] "Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members". Nucleic Acids Research 33 (12): 3875–96. 2005. doi:10.1093/nar/gki702. PMID 16027112.

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Catalytically perfect enzyme Coenzyme 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)