Summary: DNA polymerase III, theta subunit
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "DNA polymerase III holoenzyme". More...
DNA polymerase III holoenzyme Edit Wikipedia article
.jpg)
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.
Contents
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])
- 2 β units (dnaN) which act as sliding DNA clamps, they keep the polymerase bound to the DNA.
- 2 τ 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 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
- ^ 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.
- ^ 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.
- ^ 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
- Overview at Oregon State University
- DNA+Polymerase+III at the US National Library of Medicine Medical Subject Headings (MeSH)
- Clamping down on pathogenic bacteria – how to shut down a key DNA polymerase complex
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
-
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
-
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
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
| Seed (16) |
Full (202) |
Representative proteomes | UniProt (1299) |
NCBI (1917) |
Meta (3) |
||||
|---|---|---|---|---|---|---|---|---|---|
| RP15 (15) |
RP35 (67) |
RP55 (192) |
RP75 (458) |
||||||
| Jalview | |||||||||
| HTML | |||||||||
| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
| Seed (16) |
Full (202) |
Representative proteomes | UniProt (1299) |
NCBI (1917) |
Meta (3) |
||||
|---|---|---|---|---|---|---|---|---|---|
| RP15 (15) |
RP35 (67) |
RP55 (192) |
RP75 (458) |
||||||
| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| 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
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
| Model details: |
|
||||||||||||
| Model length: | 70 | ||||||||||||
| Family (HMM) version: | 11 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
Archea
|
Eukaryota
|
Bacteria
|
Other sequences
|
Viruses
|
Unclassified
|
Viroids
|
Unclassified sequence
|
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Interactions
There is 1 interaction for this family. More...
RNase_TStructures
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.
Loading structure mapping...
