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

• 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.

See also

• Central dogma of molecular biology
• Exonuclease
• Ligase
• Nuclease
• PCR
• PARP
• Reverse transcription polymerase chain reaction
• RNA ligase (ATP)

References