Polymerase
{{Short description|Class of enzymes which synthesize nucleic acid chains or polymers}}
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 [http://www.rcsb.org/pdb/cgi/explore.cgi?pid=288631034363198&pdbId=1BGX 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.
By function
| class="wikitable floatright"
|+ Classes of Template dependent polymerase ! !DNA-polymerase !RNA-polymerase |
| Template is DNA
|DNA dependent DNA-polymerase |DNA dependent RNA-polymerase |
|---|
| Template is RNA
|RNA dependent DNA polymerase |RNA dependent RNA polymerase |
- 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.{{cite journal | vauthors = Loc'h J, Rosario S, Delarue M | title = Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination | journal = Structure | volume = 24 | issue = 9 | pages = 1452–63 | date = September 2016 | pmid = 27499438 | doi = 10.1016/j.str.2016.06.014 | doi-access = free }}
- 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
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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.{{cite journal | vauthors = Hansen JL, Long AM, Schultz SC | title = Structure of the RNA-dependent RNA polymerase of poliovirus | journal = Structure | volume = 5 | issue = 8 | pages = 1109–22 | date = August 1997 | pmid = 9309225 | doi = 10.1016/S0969-2126(97)00261-X | doi-access = free }} The latter is seen in all multi-subunit RNA polymerases, in cRdRP, and in "family D" DNA polymerases found in archaea.{{cite journal | vauthors = Cramer P | title = Multisubunit RNA polymerases | journal = Current Opinion in Structural Biology | volume = 12 | issue = 1 | pages = 89–97 | date = February 2002 | pmid = 11839495 | doi = 10.1016/S0959-440X(02)00294-4 }}{{cite journal | vauthors = Sauguet L | title = The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution | journal = Journal of Molecular Biology | volume = 431 | issue = 20 | pages = 4167–4183 | date = September 2019 | pmid = 31103775 | doi = 10.1016/j.jmb.2019.05.017 | doi-access = free }} The "X" family represented by DNA polymerase beta has only a vague "palm" shape, and is sometimes considered a different superfamily ({{InterPro|IPR043519}}).{{cite journal | vauthors = Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM | title = The structure of an RNAi polymerase links RNA silencing and transcription | journal = PLoS Biology | volume = 4 | issue = 12 | pages = e434 | date = December 2006 | pmid = 17147473 | pmc=1750930 | doi = 10.1371/journal.pbio.0040434 | doi-access = free }}
Primases generally don't fall into either category. Bacterial primases usually have the Toprim domain, and are related to topoisomerases and mitochondrial helicase twinkle.{{cite journal | vauthors = Aravind L, Leipe DD, Koonin EV | title = Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins | journal = Nucleic Acids Research | volume = 26 | issue = 18 | pages = 4205–13 | date = September 1998 | pmid = 9722641 | pmc = 147817 | doi = 10.1093/nar/26.18.4205 }} 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.{{cite journal | vauthors = Iyer LM, Koonin EV, Leipe DD, Aravind L | title = Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members | journal = Nucleic Acids Research | volume = 33 | issue = 12 | pages = 3875–96 | date = 2005 | pmid = 16027112 | pmc = 1176014 | doi = 10.1093/nar/gki702 }}
File:WikiHandDNAPolII.png|Right hand structure of Bacteriophage RB69, a family B DdRP.
See also
References
{{Reflist}}
External links
{{DNA replication}}
{{Kinases}}
{{Enzymes}}
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