DNA polymerase III holoenzyme

Pol III can also refer to HNoMS Pol III, a Norwegian guard vessel from WWII

DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg (son of Arthur Kornberg) and Malcolm Gefter in 1970. The complex has high processivity (i.e. the number of nucleotides added per binding event) and, specifically referring to the replication of the E.coli genome, works in conjunction with four other DNA polymerases (Pol I, Pol II, Pol IV, and Pol V). Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that correct replication mistakes by means of exonuclease activity working 3'->5'. DNA Pol III is a component of the replisome, which is located at the replication fork.

Components

Bacterial DNA polymerase III alpha subunit
Identifiers
Symbol	DNA_pol3_alpha
Pfam	PF07733
InterPro	IPR011708
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

DNA polymerase III, delta subunit
atpgs bound e. coli clamp loader complex
Identifiers
Symbol	DNA_pol3_delta
Pfam	PF06144
Pfam clan	CL0023
InterPro	IPR010372
SCOP	1jql
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

DNA polymerase III, delta subunit, C terminal
adp bound e. coli clamp loader complex
Identifiers
Symbol	DNApol3-delta_C
Pfam	PF09115
InterPro	IPR015199
SCOP	1a5t
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

DNA polymerase III subunits tau domain IV DnaB-binding
Identifiers
Symbol	DNA_pol3_tau_4
Pfam	PF12168
InterPro	IPR022001
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

DNA polymerase III tau subunit V interacting with alpha
Identifiers
Symbol	DNA_pol3_tau_5
Pfam	PF12170
InterPro	IPR021029
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

DNA polymerase III, theta subunit
structure of the e. coli pol iii epsilon-hot proofreading complex
Identifiers
Symbol	DNA_pol3_theta
Pfam	PF06440
InterPro	IPR009052
SCOP	1du2
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

DNA polymerase III chi subunit, HolC
crystal structure of chi and psi subunit heterodimer from dna pol iii
Identifiers
Symbol	DNA_pol3_chi
Pfam	PF04364
InterPro	IPR007459
SCOP	1em8
Available protein structures: Pfam structures PDB RCSB PDB; PDBe PDBsum structure summary

The replisome is composed of the following:

• 2 DNA Pol III enzymes, each comprising α, ε and θ subunits.
  • the α subunit has the polymerase activity.
  • the ε subunit as 3'-5' exonuclease activity.
  • the θ subunit stimulates the ε subunit's proofreading.
• 2 β units which act as sliding DNA clamps, they keep the polymerase bound to the DNA.
• 2 τ units which acts to dimerize two of the core enzymes (α, ε, and θ subunits).
• 1 γ unit which acts as a clamp loader for the lagging strand Okazaki fragments, helping the two β subunits to form a unit and bind to DNA. The γ unit is made up of 5 γ subunits which include 3 γ subunits, 1 δ subunit, and 1 δ' subunit. The δ is involved in copying of the lagging strand.
• Χ and Ψ which form a 1:1 complex and bind to γ or τ.^[1]

Activity

DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second.^[2] DNA Pol III activity begins after strand separation at the origin of replication. Because DNA synthesis cannot start de novo, an RNA primer, complementary to part of the single-stranded DNA, is synthesized by primase (an RNA polymerase):

("!" for RNA, '"$" for DNA, "*" for polymerase)

--------> 
         * * * *
! ! ! !  _ _ _ _    
_ _ _ _ | RNA   |   <--ribose (sugar)-phosphate backbone
G U A U | Pol   |   <--RNA primer
* * * * |_ _ _ _|   <--hydrogen bonding
C A T A G C A T C C <--template ssDNA (single-stranded DNA)
_ _ _ _ _ _ _ _ _ _ <--deoxyribose (sugar)-phosphate backbone
$ $ $ $ $ $ $ $ $ $

Addition onto 3'OH

As replication progresses and the replisome moves forward, DNA polymerase III arrives at the RNA primer and begins replicating the DNA, adding onto the 3'OH of the primer:

         * * * *
! ! ! !  _ _ _ _
_ _ _ _ | DNA   |   <--ribose (sugar)-phosphate backbone
G U A U | Pol   |   <--RNA primer
* * * * |_III_ _|   <--hydrogen bonding
C A T A G C A T C C <--template ssDNA (single-stranded DNA)
_ _ _ _ _ _ _ _ _ _ <--deoxyribose (sugar)-phosphate backbone
$ $ $ $ $ $ $ $ $ $

Synthesis of DNA

DNA polymerase III will then synthesize a continuous or discontinuous strand of DNA, depending if this is occurring on the leading or lagging strand (Okazaki fragment) of the DNA. DNA polymerase III has a high processivity and therefore, synthesizes DNA very quickly. This high processivity is due in part to the β-clamps that "hold" onto the DNA strands.

        ----------->
                    * * * *
! ! ! ! $ $ $ $ $ $ _ _ _ _
_ _ _ _ _ _ _ _ _ _| DNA   |   <--deoxyribose (sugar)-phosphate backbone
G U A U C G T A G G| Pol   |   <--RNA primer
* * * * * * * * * *|_III_ _|   <--hydrogen bonding
C A T A G C A T C C <--template ssDNA (single-stranded DNA)
_ _ _ _ _ _ _ _ _ _ <--deoxyribose (sugar)-phosphate backbone
$ $ $ $ $ $ $ $ $ $

Removal of primer

After replication of the desired region, the RNA primer is removed by DNA polymerase I via the process of nick translation. The removal of the RNA primer allows DNA ligase to ligate the DNA-DNA nick between the new fragment and the previous strand. DNA polymerase I & III, along with many other enzymes are all required for the high fidelity, high-processivity of DNA replication.

See also

• DNA replication
• DNA polymerase

References

1. ^ Olson, M. W.; Dallmann, H. G.; McHenry, C. S. (1995). "DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' to a physiologically relevant range". The Journal of biological chemistry 270 (49): 29570–29577. PMID 7494000.  edit
2. ^ Kelman, Z.; O'Donnell, M. (1995). "Dna Polymerase III Holoenzyme: Structure and Function of a Chromosomal Replicating Machine". Annual Review of Biochemistry 64: 171. doi:10.1146/annurev.bi.64.070195.001131.  edit

External links

• Overview at Oregon State University
• MeSH DNA+Polymerase+III