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8  structures 151  species 1  interaction 202  sequences 3  architectures

Family: DNA_pol3_theta (PF06440)

Summary: DNA polymerase III, theta subunit

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

DNA polymerase III holoenzyme Edit Wikipedia article

"Pol III" redirects here. For the Norwegian guard vessel from WWII, see HNoMS Pol III.
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 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. X can also mediate the switch from RNA primer to DNA.[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   |   <--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

References

  1. ^ Reyes-Lamothe R, Sherratt D, Leake M (2010). "Stoichiometry and Architecture of Active DNA Replication Machinery in Escherichia Coli". Science. 328: 498–501. doi:10.1126/science.1185757. PMC 2859602 Freely accessible. 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 delta.delta' 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/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, theta subunit Provide feedback

DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit. The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helices while the C-terminal third is disordered [1]. The function of the theta subunit is poorly understood, but the interaction of the theta subunit with the epsilon subunit is thought to enhance the 3' to 5' exonucleolytic proofreading activity of epsilon [2].

Literature references

  1. Keniry MA, Berthon HA, Yang JY, Miles CS, Dixon NE; , Protein Sci 2000;9:721-733.: NMR solution structure of the theta subunit of DNA polymerase III from Escherichia coli. PUBMED:10794414 EPMC:10794414

  2. DeRose EF, Darden T, Harvey S, Gabel S, Perrino FW, Schaaper RM, London RE; , Biochemistry 2003;42:3635-3644.: Elucidation of the epsilon-theta subunit interface of Escherichia coli DNA polymerase III by NMR spectroscopy. PUBMED:12667053 EPMC:12667053

Internal database links

SCOOP: DUF3283

External database links

SCOP: 1du2

This tab holds annotation information from the InterPro database.

InterPro entry IPR009052

This entry represents the theta subunit of DNA polymerase III from bacteria, whose core structure consists of an irregular array of three helices [PUBMED:10794414].

DNA polymerase III (Pol III) is the primary enzyme responsible for replication of Escherichia coli chromosomal DNA. The holoenzyme consists of 17 proteins and contains two core polymerases. The Pol III catalytic core has three tightly associated subunits: alpha, epsilon and theta. The alpha subunit is responsible for the DNA polymerase activity, while the epsilon subunit is the 3'-5' proofreading exonuclease. The epsilon subunit binds to both the alpha and theta subunits in the linear order alpha-epsilon-theta. The theta subunit is the smallest, and may act to enhance the proofreading activity of epsilon, especially under extreme conditions [PUBMED:16753031].

This entry also includes a homologue of polymerase III theta called HOT (homologue of theta) from Bacteriophage P1. HOT contains three alpha-helices, as reported for theta, but the folding topology of the two is different, which could account for the suggested greater heat stability of HOT as compared to theta [PUBMED:15576035].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function DNA-directed DNA polymerase activity (GO:0003887)
DNA binding (GO:0003677)
Biological process DNA replication (GO:0006260)

Domain organisation

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Alignments

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(16)		 Full
(202)		 Representative proteomes UniProt
(1299)		 NCBI
(1917)		 Meta
(3)
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(15)		 RP35
(67)		 RP55
(192)		 RP75
(458)
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  Seed
(16)		 Full
(202)		 Representative proteomes UniProt
(1299)		 NCBI
(1917)		 Meta
(3)
RP15
(15)		 RP35
(67)		 RP55
(192)		 RP75
(458)
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  Seed
(16)		 Full
(202)		 Representative proteomes UniProt
(1299)		 NCBI
(1917)		 Meta
(3)
RP15
(15)		 RP35
(67)		 RP55
(192)		 RP75
(458)
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Curation and family details

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Seed source: Pfam-B_27631 (release 9.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 16
Number in full: 202
Average length of the domain: 68.00 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 85.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 34.4 34.4
Trusted cut-off 34.4 35.5
Noise cut-off 34.1 34.3
Model length: 70
Family (HMM) version: 11
Download: download the raw HMM for this family

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Interactions

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

RNase_T

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 DNA_pol3_theta domain has been found. There are 8 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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