Polymerase

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.

## Contents

* 1 Types
* 1.1 By function
* 1.2 By structure
* 2 See also
* 3 References
* 4 External links

## 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

* 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.[1]
* 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

### 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.

## See also

* Central dogma of molecular biology
* Exonuclease
* Ligase
* Nuclease
* PCR
* PARP
* Reverse transcription polymerase chain reaction
* RNA ligase (ATP)

## 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

* v
* t
* e

DNA replication (comparing Prokaryotic to Eukaryotic)

Initiation|

| Prokaryotic
(initiation)|

* Pre-replication complex

* dnaC
* Cdc6

* Helicase
* dnaA
* dnaB
* T7

* Primase
* dnaG

|

Eukaryotic
(preparation in
G1 phase)|

* Pre-replication complex

* Origin recognition complex
* ORC1
* ORC2
* ORC3
* ORC4
* ORC5
* ORC6

* Cdc6

* Cdt1

* Minichromosome maintenance
* MCM2
* MCM3
* MCM4
* MCM5
* MCM6
* MCM7

* Licensing factor

* Autonomously replicating sequence

* Single-strand binding protein
* SSBP2
* SSBP3
* SSBP4

* RNase H
* RNASEH1
* RNASEH2A

* Helicase: HFM1

* Primase: PRIM1
* PRIM2

Both|

* Origin of replication/Ori/Replicon

* Replication fork
* Lagging and leading strands
* Okazaki fragments
* Primer

Replication|

| Prokaryotic
(elongation)|

* DNA polymerase III holoenzyme
* dnaC
* dnaE
* dnaH
* dnaN
* dnaQ
* dnaT
* dnaX
* holA
* holB
* holC
* holD
* holE
*   * Replisome
* DNA ligase
* DNA clamp
* Topoisomerase
* DNA gyrase

* Prokaryotic DNA polymerase: DNA polymerase I
* Klenow fragment

|

Eukaryotic
(synthesis in
S phase)|

* Replication factor C
* RFC1
* Flap endonuclease
* FEN1
* Topoisomerase
* Replication protein A
* RPA1

* Eukaryotic DNA polymerase:
* alpha
* POLA1
* POLA2
* PRIM1
* PRIM2
* delta
* POLD1
* POLD2
* POLD3
* POLD4
* epsilon
* POLE
* POLE2
* POLE3
* POLE4

* DNA clamp
* PCNA

* Control of chromosome duplication

Both|

* Movement: Processivity
* DNA ligase

Termination|

* Telomere: Telomerase
* TERT
* TERC
* DKC1

* v
* t
* e

Transferases: phosphorus-containing groups (EC 2.7)

2.7.1-2.7.4:
phosphotransferase/kinase
(PO4)|

| 2.7.1: OH acceptor|

* Hexo-
* Gluco-
* Fructo-
* Hepatic
* Galacto-
* Phosphofructo-
* 1
* Liver
* Muscle
* Platelet
* 2
* Riboflavin
* Shikimate
* Thymidine
* ADP-thymidine
* NAD+
* Glycerol
* Pantothenate
* Mevalonate
* Pyruvate
* Deoxycytidine
* PFP
* Diacylglycerol
* Phosphoinositide 3
* Class I PI 3
* Class II PI 3
* Sphingosine
* Glucose-1,6-bisphosphate synthase

|

2.7.2: COOH acceptor|

* Phosphoglycerate
* Aspartate kinase

2.7.3: N acceptor|

* Creatine

2.7.4: PO4 acceptor|

* Phosphomevalonate
* Adenylate
* Nucleoside-diphosphate
* Uridylate
* Guanylate
* Thiamine-diphosphate

2.7.6: diphosphotransferase
(P2O7)|

* Ribose-phosphate diphosphokinase
* Thiamine diphosphokinase

2.7.7: nucleotidyltransferase
(PO4-nucleoside)|

| Polymerase|

| DNA polymerase|

DNA-directed DNA polymerase
I/A

Taq
II/B

Pfu
III/C
IV/X

TDT
V/Y

RNA-directed DNA polymerase
Reverse transcriptase

Telomerase

|

RNA nucleotidyltransferase|

Template-directed
RNA polymerase I

III

ssRNAP

POLRMT
Primase

PrimPol
RNA-dependent RNA polymerase
Polyadenylation
PAP
PNPase

Phosphorolytic
3' to 5' exoribonuclease|

* RNase PH
* PNPase

Nucleotidyltransferase|

* UTP—glucose-1-phosphate uridylyltransferase
* Galactose-1-phosphate uridylyltransferase

Guanylyltransferase|

* mRNA capping enzyme

Other|

* Recombinase (Integrase)
* Transposase

2.7.8: miscellaneous|

| Phosphatidyltransferases|

* CDP-diacylglycerol—glycerol-3-phosphate 3-phosphatidyltransferase
* CDP-diacylglycerol—serine O-phosphatidyltransferase
* CDP-diacylglycerol—inositol 3-phosphatidyltransferase
* CDP-diacylglycerol—choline O-phosphatidyltransferase

|

Glycosyl-1-phosphotransferase|

* N-acetylglucosamine-1-phosphate transferase

2.7.10-2.7.13: protein kinase
(PO4; protein acceptor)|

| 2.7.10: protein-tyrosine|

* see tyrosine kinases

|

2.7.11: protein-serine/threonine|

* see serine/threonine-specific protein kinases

2.7.12: protein-dual-specificity|

* see serine/threonine-specific protein kinases

2.7.13: protein-histidine|

* Protein-histidine pros-kinase
* Protein-histidine tele-kinase
* Histidine kinase

* v
* t
* e

Enzymes

Activity|

* Active site
* Binding site
* Catalytic triad
* Oxyanion hole
* Enzyme promiscuity
* Catalytically perfect enzyme
* Coenzyme
* Cofactor
* Enzyme catalysis

Regulation|

* Allosteric regulation
* Cooperativity
* Enzyme inhibitor
* Enzyme activator

Classification|

* EC number
* Enzyme superfamily
* Enzyme family
* List of enzymes

Kinetics|

* Enzyme kinetics
* Eadie–Hofstee diagram
* Hanes–Woolf plot
* Lineweaver–Burk plot
* Michaelis–Menten kinetics

Types|

* EC1 Oxidoreductases (list)
* EC2 Transferases (list)
* EC3 Hydrolases (list)
* EC4 Lyases (list)
* EC5 Isomerases (list)
* EC6 Ligases (list)
* EC7 Translocases (list)

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