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.

Structure of Taq DNA polymerase

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

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

See also

References
  1. Loc'h J, Rosario S, Delarue M (September 2016). "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination". Structure. 24 (9): 1452–63. doi:10.1016/j.str.2016.06.014. PMID 27499438.
  2. Hansen JL, Long AM, Schultz SC (August 1997). "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure. 5 (8): 1109–22. doi:10.1016/S0969-2126(97)00261-X. PMID 9309225.
  3. Cramer P (February 2002). "Multisubunit RNA polymerases". Current Opinion in Structural Biology. 12 (1): 89–97. doi:10.1016/S0959-440X(02)00294-4. PMID 11839495.
  4. Sauguet L (September 2019). "The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution". Journal of Molecular Biology. 431 (20): 4167–4183. doi:10.1016/j.jmb.2019.05.017. PMID 31103775.
  5. Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM (December 2006). "The structure of an RNAi polymerase links RNA silencing and transcription". PLoS Biology. 4 (12): e434. doi:10.1371/journal.pbio.0040434. PMC 1750930. PMID 17147473.
  6. Aravind L, Leipe DD, Koonin EV (September 1998). "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. doi:10.1093/nar/26.18.4205. PMC 147817. PMID 9722641.
  7. Iyer LM, Koonin EV, Leipe DD, Aravind L (2005). "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. doi:10.1093/nar/gki702. PMC 1176014. PMID 16027112.
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