View source for Biology:Polymerase

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

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

A DNA polymerase from the [[Earth:Thermophile|thermophilic]] bacterium, ''[[Biology:Thermus aquaticus|Thermus aquaticus]]'' (''Taq'') ([[Biology: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 [[Biology:Polymerase chain reaction|polymerase chain reaction]], an important technique of [[Biology:Molecular biology|molecular biology]].

A polymerase may be template-dependent or template-independent.  [[Biology:Polynucleotide adenylyltransferase|Poly-A-polymerase]] is an example of template independent polymerase.  [[Biology:Terminal deoxynucleotidyl transferase|Terminal deoxynucleotidyl transferase]] also known to have template independent and template dependent activities.

==Types==

=== 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 [[Biology:Reverse transcriptase|Reverse transcriptase]]
|RNA dependent RNA polymerase <br/> or [[Biology:RNA-dependent RNA polymerase|RdRp or RNA-replicase]]
|}
*[[Biology:DNA polymerase|DNA polymerase]] (DNA-directed DNA polymerase, DdDP)
**Family A: [[Biology:DNA polymerase I|DNA polymerase I]]; Pol [[Biology:POLG|γ]], θ, [[Biology:DNA polymerase nu|ν]]
**Family B: [[Biology:DNA polymerase II|DNA polymerase II]]; Pol [[Biology:DNA polymerase alpha|α]], [[Biology:DNA polymerase delta|δ]], [[Biology:DNA polymerase epsilon|ε]], [[Biology:REV3L|ζ]]
**Family C: [[Biology:DNA polymerase III holoenzyme|DNA polymerase III holoenzyme]]
**Family X: Pol [[Biology:DNA polymerase beta|β]], [[Biology:DNA polymerase lambda|λ]], [[Biology:DNA polymerase mu|μ]]
***[[Biology:Terminal deoxynucleotidyl transferase|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: [[Biology:DNA polymerase IV|DNA polymerase IV]] (DinB) and [[Biology:DNA polymerase V|DNA polymerase V]] (UmuD'2C) - [[Biology:SOS response|SOS]] repair polymerases; Pol [[Biology:DNA polymerase eta|η]], [[Biology:POLI|ι]], [[Biology:POLK|κ]]
*[[Biology:Reverse transcriptase|Reverse transcriptase]] (RT; RNA-directed DNA polymerase; RdDP)
** [[Biology:Telomerase|Telomerase]]
*DNA-directed [[Biology:RNA polymerase|RNA polymerase]] (DdRP, RNAP)
**Multi-subunit (msDdRP): [[Biology:RNA polymerase I|RNA polymerase I]], [[Biology:RNA polymerase II|RNA polymerase II]], [[Biology:RNA polymerase III|RNA polymerase III]]
**Single-subunit (ssDdRP): [[Biology:T7 RNA polymerase|T7 RNA polymerase]], [[Biology:POLRMT|POLRMT]]
**[[Biology:Primase|Primase]], [[Biology:PrimPol|PrimPol]]
*RNA replicase (RNA-directed RNA polymerase, RdRP)
**Viral (single-subunit)
**Eukaryotic cellular (cRdRP; dual-subunit)
*Template-less RNA elongation
** [[Biology:Polyadenylation|Polyadenylation]]: [[Biology:Polynucleotide adenylyltransferase|PAP]], [[Biology:Polynucleotide phosphorylase|PNPase]]
{{clear|right}}

=== By structure ===
Polymerases are generally split into two superfamilies, the "right hand" fold ({{InterPro|IPR043502}}) and the "double psi [[Biology:Beta barrel|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 [[Biology:DNA polymerase beta|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 [[Biology:Topoisomerase|topoisomerase]]s and mitochondrial helicase 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.
<!-- need barrel -->
<!-- need toprim -->
<!-- need AEP -->
</gallery>

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

== References ==
{{Reflist}}

==External links==

{{DNA replication}}
{{Kinases}}
{{Enzymes}}

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

{{Sourceattribution|Polymerase}}