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15  structures 1623  species 0  interactions 1719  sequences 4  architectures

Family: DNApol3-delta_C (PF09115)

Summary: DNA polymerase III, delta subunit, C terminal

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This is the Wikipedia entry entitled "DNA polymerase III holoenzyme". More...

DNA polymerase III holoenzyme Edit Wikipedia article

Schematic picture of DNA polymerase III* (with subunits).

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 corrects replication mistakes by means of exonuclease activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the replisome, which is located at the replication fork.


The replisome is composed of the following:

  • 2 DNA Pol III enzymes, each comprising α, ε and θ subunits. (It has been proven that there is a third copy of Pol III at the replisome.[1])
    • the α subunit (encoded by the dnaE gene) has the polymerase activity.
    • the ε subunit (dnaQ) has 3'→5' exonuclease activity.
    • the θ subunit (holE) stimulates the ε subunit's proofreading.
  • 2 β units (dnaN) which act as sliding DNA clamps, they keep the polymerase bound to the DNA.
  • 2 Ï„ units (dnaX) which act to dimerize two of the core enzymes (α, ε, and θ subunits).
  • 1 γ unit (also dnaX) 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 (holA), and 1 δ' subunit (holB). The δ is involved in copying of the lagging strand.
  • Χ (holC) and Ψ (holD) which form a 1:1 complex and bind to γ or Ï„. X can also mediate the switch from RNA primer to DNA.[2]


DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second.[3] 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   |   <--deoxyribose (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


  1. ^ Reyes-Lamothe R, Sherratt D, Leake M (2010). "Stoichiometry and Architecture of Active DNA Replication Machinery in Escherichia Coli". Science. 328 (5977): 498–501. doi:10.1126/science.1185757. PMC 2859602. PMID 20413500.
  2. ^ Olson MW, Dallmann HG, McHenry CS (December 1995). "DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for' to a physiologically relevant range". J. Biol. Chem. 270 (49): 29570–7. doi:10.1074/jbc.270.49.29570. PMID 7494000.
  3. ^ Kelman Z, O'Donnell M (1995). "DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine". Annu. Rev. Biochem. 64: 171–200. doi:10.1146/ PMID 7574479.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DNA polymerase III, delta subunit, C terminal Provide feedback

Members of this family, which are predominantly found in prokaryotic DNA polymerase III, assume an alpha helical structure, with a core of five alpha helices, and an additional small helix. They are essential for the formation of the polymerase clamp loader [1].

Literature references

  1. Guenther B, Onrust R, Sali A, O'Donnell M, Kuriyan J; , Cell. 1997;91:335-345.: Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. PUBMED:9363942 EPMC:9363942

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015199

This entry represents a domain which is predominantly found in prokaryotic DNA polymerase III, assuming an alpha helical structure with a core of five alpha helices and an additional small helix. This domain is essential for the formation of the polymerase clamp loader [ PUBMED:9363942 ].

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan post-AAA (CL0604), which has the following description:

According to SCOP this superfamily contains a 5 helical bundle domain that is found to the C-terminus of a P-loop AAA domain.

The clan contains the following 5 members:

DNA_pol3_delt_C DNA_pol3_gamma3 DNApol3-delta_C MgsA_C Rep_fac_C


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Curation and family details

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Seed source: pdb_1a5t
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sammut SJ
Number in seed: 49
Number in full: 1719
Average length of the domain: 108.70 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 32.07 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 117
Family (HMM) version: 12
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DNApol3-delta_C domain has been found. There are 15 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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