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11  structures 4065  species 5  interactions 4182  sequences 10  architectures

Family: DNA_pol3_delta (PF06144)

Summary: DNA polymerase III, delta subunit

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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 Provide feedback

DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [1]. The delta subunit is also known as HolA.

Literature references

  1. Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry CS; , J Biol Chem 2001;276:35165-35175.: The delta and delta ' subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. PUBMED:11432857 EPMC:11432857


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010372

DNA polymerase III, delta subunit (EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [PUBMED:11432857]. The delta subunit is also known as HolA.

Gene Ontology

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

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 198 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_4 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_2 Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arch_ATPase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 Bac_DnaA CbiA CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1253 DUF1611 DUF2075 DUF2478 DUF258 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GTP_EFTU GTP_EFTU_D2 GTP_EFTU_D4 Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK IIGP IPPT IPT IstB_IS21 KaiC KAP_NTPase Kinesin Kinesin-relat_1 Kinesin-related KTI12 LpxK MCM MEDS Mg_chelatase Mg_chelatase_2 MipZ Miro MMR_HSR1 MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind UPF0079 UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YhjQ Zeta_toxin Zot

Alignments

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  Seed
(24)
Full
(4182)
Representative proteomes NCBI
(3675)
Meta
(1752)
RP15
(308)
RP35
(602)
RP55
(775)
RP75
(910)
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  Seed
(24)
Full
(4182)
Representative proteomes NCBI
(3675)
Meta
(1752)
RP15
(308)
RP35
(602)
RP55
(775)
RP75
(910)
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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 View help on the curation process

Seed source: Pfam-B_9452 (release 9.0)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 24
Number in full: 4182
Average length of the domain: 168.00 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 49.90 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 172
Family (HMM) version: 8
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Species distribution

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Interactions

There are 5 interactions for this family. More...

DNApol3-delta_C AAA DNA_pol3_delta DNA_pol3_beta_3 DNA_pol3_beta_2

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_delta domain has been found. There are 11 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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