Editing Polymerase

{{Short description|Class of enzymes which synthesize nucleic acid chains or polymers}}
[[Image:Taq polimerase.png|thumb|Structure of [[Taq polymerase|Taq DNA polymerase]]]]

In [[biochemistry]], a '''polymerase''' is an [[enzyme]] ([[Enzyme Commission number|EC]] 2.7.7.6/7/19/48/49) that synthesizes long chains of [[polymer]]s or [[nucleic acid]]s. [[DNA polymerase]] and [[RNA polymerase]] are used to assemble [[DNA]] and [[RNA]] molecules, respectively, by copying a DNA template strand using [[Base pair|base-pairing]] interactions or RNA by half ladder replication.

A DNA polymerase from the [[thermophile|thermophilic]] bacterium, ''[[Thermus aquaticus]]'' (''Taq'') ([[Protein Data Bank|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.  [[Polynucleotide adenylyltransferase|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 <br/> or common [[DNA polymerases]]
|DNA dependent RNA-polymerase <br/> or common [[RNA polymerases]]
|-
!Template is RNA
|RNA dependent DNA polymerase <br/> or [[Reverse transcriptase]]
|RNA dependent RNA polymerase <br/> or [[RNA-dependent RNA polymerase|RdRp or RNA-replicase]]
|}
*[[DNA polymerase]] (DNA-directed DNA polymerase, DdDP)
**Family A: [[DNA polymerase I]]; Pol [[POLG|γ]], [[POLQ|θ]], [[DNA polymerase nu|ν]]
**Family B: [[DNA polymerase II]]; Pol [[DNA polymerase alpha|α]], [[DNA polymerase delta|δ]], [[DNA polymerase epsilon|ε]], [[REV3L|ζ]]
**Family C: [[DNA polymerase III holoenzyme]]
**Family X: Pol [[DNA polymerase beta|β]], [[DNA polymerase lambda|λ]], [[DNA polymerase mu|μ]]
***[[Terminal deoxynucleotidyl transferase]] (TDT), which lends diversity to antibody heavy chains.<ref>{{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 }}</ref>
**Family Y: [[DNA polymerase IV]] (DinB) and [[DNA polymerase V]] (UmuD'2C) - [[SOS response|SOS]] repair polymerases; Pol [[DNA polymerase eta|η]], [[POLI|ι]], [[POLK|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]]: [[Polynucleotide adenylyltransferase|PAP]], [[Polynucleotide phosphorylase|PNPase]]
{{clear|right}}

== 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.<ref name="pmid9309225">{{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 }}</ref> The latter is seen in all multi-subunit RNA polymerases, in cRdRP, and in "family D" DNA polymerases found in archaea.<ref name="pmid11839495">{{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 }}</ref><ref name=qde1-mono>{{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 }}</ref> The "X" family represented by [[DNA polymerase beta]] has only a vague "palm" shape, and is sometimes considered a different superfamily ({{InterPro|IPR043519}}).<ref>{{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 }}</ref>

Primases generally don't fall into either category. Bacterial primases usually have the Toprim domain, and are related to [[topoisomerase]]s and mitochondrial helicase [[Twinkle (protein)|twinkle]].<ref>{{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 }}</ref> 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.<ref>{{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 }}</ref>

<gallery>
File:WikiHandDNAPolII.png|Right hand structure of Bacteriophage RB69, a family B DdRP.
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</gallery>

==See also==
* [[Central dogma of molecular biology]]
* [[Exonuclease]]
* [[Ligase]]
* [[Nuclease]]
* [[Polymerase chain reaction|PCR]]
* [[Poly (ADP-ribose) polymerase|PARP]]
* [[Reverse transcription polymerase chain reaction]]
* [[RNA ligase (ATP)]]

== References ==
{{Reflist}}

==External links==

{{DNA replication}}
{{Kinases}}
{{Enzymes}}
{{Portal bar|Biology|border=no}}
{{Authority control}}

[[Category:EC 2.7.7]]
[[Category:Enzymes]]