Biology:Polymerase

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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

By structure

Polymerases are generally split into two superfamilies, the "right hand" fold (InterProIPR043502) 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 (InterProIPR043519).[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]

See also

References

  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. 
  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. 
  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. 
  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. 

External links