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9  structures 811  species 1  interaction 817  sequences 2  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).
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

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 τ units (dnaX) which acts 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 τ.[2]

Activity

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   |   <--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

References

  1. ^ DOI: 10.1126/science.1185757
  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 delta.delta' to a physiologically relevant range". J. Biol. Chem. 270 (49): 29570–7. 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/annurev.bi.64.070195.001131. 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


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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Alignments

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Full
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Representative proteomes NCBI
(453)
Meta
(22)
RP15
(20)
RP35
(42)
RP55
(70)
RP75
(97)
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  Seed
(41)
Full
(817)
Representative proteomes NCBI
(453)
Meta
(22)
RP15
(20)
RP35
(42)
RP55
(70)
RP75
(97)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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Curation View help on the curation process

Seed source: pdb_1a5t
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 41
Number in full: 817
Average length of the domain: 117.10 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 36.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.7 21.9
Noise cut-off 21.6 21.6
Model length: 119
Family (HMM) version: 5
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Species distribution

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Interactions

There is 1 interaction for this family. More...

DNA_pol3_delta

Structures

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 9 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 seqence.

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