DNA polymerase III holoenzyme

DNAポリメラーゼIIIホロ酵素

WordNet

1. the 9th letter of the Roman alphabet (同)i
2. the 4th letter of the Roman alphabet (同)d
3. an enzyme that catalyzes the formation of new DNA and RNA from an existing strand of DNA or RNA

PrepTutorEJDIC

1. 『私は』私が
2. iodineの化学記号
3. deuteriumの化学記号
4. deoxyribonucleic acidディオキシリボ核酸

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/04/17 00:02:36」(JST)

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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.)
  • 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.

Activity

DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second. 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
• Beta clamp
• Clamping down on pathogenic bacteria – how to shut down a key DNA polymerase complex

References

External links

• Overview at Oregon State University
• DNA Polymerase III at the US National Library of Medicine Medical Subject Headings (MeSH)

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English Journal

• Plasmid replication initiator interactions with origin 13-mers and polymerase subunits contribute to strand-specific replisome assembly.

• Wawrzycka A1, Gross M1, Wasaznik A1, Konieczny I2.
• Proceedings of the National Academy of Sciences of the United States of America.Proc Natl Acad Sci U S A.2015 Jul 20. pii: 201504926. [Epub ahead of print]
• Although the molecular basis for replisome activity has been extensively investigated, it is not clear what the exact mechanism for de novo assembly of the replication complex at the replication origin is, or how the directionality of replication is determined. Here, using the plasmid RK2 replicon,
• PMID 26195759

• DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection.

• Lindow JC1, Dohrmann PR1, McHenry CS2.
• The Journal of biological chemistry.J Biol Chem.2015 Jul 3;290(27):16851-60. doi: 10.1074/jbc.M115.661090. Epub 2015 May 18.
• Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first ste
• PMID 25987558

• The POLD3 subunit of DNA polymerase δ can promote translesion synthesis independently of DNA polymerase ζ.

• Hirota K1, Yoshikiyo K2, Guilbaud G3, Tsurimoto T4, Murai J5, Tsuda M2, Phillips LG3, Narita T2, Nishihara K2, Kobayashi K6, Yamada K7, Nakamura J8, Pommier Y4, Lehmann A9, Sale JE10, Takeda S11.
• Nucleic acids research.Nucleic Acids Res.2015 Feb 18;43(3):1671-83. doi: 10.1093/nar/gkv023. Epub 2015 Jan 27.
• The replicative DNA polymerase Polδ consists of a catalytic subunit POLD1/p125 and three regulatory subunits POLD2/p50, POLD3/p66 and POLD4/p12. The ortholog of POLD3 in Saccharomyces cerevisiae, Pol32, is required for a significant proportion of spontaneous and UV-induced mutagenesis through its a
• PMID 25628356

Japanese Journal

• The dnaE173 mutator mutation confers on the α subunit of Escherichia coli DNA polymerase III a capacity for highly processive DNA synthesis and stable binding to primer/template DNA

• Yanagihara Fusamitsu,Yoshida Shohei,Sugaya Yutaka [他],MAKI Hisaji
• Genes & genetic systems 82(4), 273-280, 2007-08-25
• … The strong mutator mutation dnaE173 which causes an amino-acid substitution in the α subunit of DNA polymerase III is unique in its ability to induce sequence-substitution mutations. … We showed previously that multiple biochemical properties of DNA polymerase III holoenzyme of Escherichia coli are simultaneously affected by the dnaE173 mutation. …
• NAID 10024394579

• DNA polymerase III holoenzyme : structure and function of a chromosomal replicating machine

• KELMAN Z.
• Annu. Rev. Biochem 64, 171-200, 1995
• NAID 80008391395

• Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme : a sliding DNA clamp

• KONG X. P.
• Cell 69, 425-437, 1992
• NAID 30010691246

Related Links

• DNA_polymerase_III_holoenzyme

DNA polymerase III holoenzyme Pol III can also refer to KNM Pol III, a Norwegian guard vessel from WW2 DNA polymerase III holoenzyme is the primary enzyme ... my.chemeurope.com With an accout for my.chemeurope.com you ...

• DNA polymerase III holoenzyme - wikidoc

Pol III can also refer to KNM Pol III, a Norwegian guard vessel from WW2 DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg (son of Arthur ...

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★リンクテーブル★

リンク元	「DNAポリメラーゼIIIホロ酵素」
関連記事	「D」「II」「I」「DNA」

「DNAポリメラーゼIIIホロ酵素」

　　[★]

英

DNA polymerase III holoenzyme

同

Pol IIIホロ酵素

関

[[]]

「D」

　　[★]

• アスパラギン酸
• ジヒドロウリジン
• 遠位の distal,
• うつ病 depression
• 下行結腸 descending colon(大腸内視鏡検査の結果を記載するときに用いる)

　 　

「II」

　　[★]

• 蛍光像増倍管 image intensifier
• インスリン分泌指数 インスリノゲニック・インデックス insulinogenic index
• 黄疸指数 icterus index

「I」

　　[★]

• イソロイシン isoleucine
• イノシン inosine
• 阻害剤 inhibitor
• iodine
• ヨード iodide
• I因子 factor I

　 　 　

「DNA」

　　[★]

英

deoxyribonucleic acid

同

デオキシリボ核酸

関

リボ核酸 RNA