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P28630

- HOLA_ECOLI

UniProt

P28630 - HOLA_ECOLI

Protein

DNA polymerase III subunit delta

Gene

holA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (09 Jul 2014)
      Sequence version 1 (01 Dec 1992)
      Previous versions | rss
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    Functioni

    DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA.

    Catalytic activityi

    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

    GO - Molecular functioni

    1. DNA binding Source: InterPro
    2. DNA-directed DNA polymerase activity Source: UniProtKB-KW
    3. protein binding Source: IntAct

    GO - Biological processi

    1. DNA-dependent DNA replication Source: EcoCyc

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA replication

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11412-MONOMER.
    ECOL316407:JW0635-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase III subunit delta (EC:2.7.7.7)
    Gene namesi
    Name:holA
    Ordered Locus Names:b0640, JW0635
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11412. holA.

    Subcellular locationi

    GO - Cellular componenti

    1. DNA polymerase III complex Source: EcoCyc

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 343343DNA polymerase III subunit deltaPRO_0000105505Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriP28630.

    Interactioni

    Subunit structurei

    The DNA polymerase holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential subassemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core (subunits alpha,epsilon and theta) contains the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. This complex contains delta, delta', psi and chi, and copies of either or both of two different DnaX proteins, gamma and tau. The composition of the holoenzyme is, therefore: (alpha,epsilon,theta)[2]-(gamma/tau)[3]-delta,delta', psi,chi-beta[4].

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    dnaEP104434EBI-549153,EBI-549111
    dnaNP0A98810EBI-549153,EBI-542385
    dnaXP06710-15EBI-549153,EBI-6464728
    holBP2863117EBI-549153,EBI-549161
    mutLP233672EBI-549153,EBI-554913
    nfsAP171173EBI-549153,EBI-1120624
    yeeWP645262EBI-549153,EBI-9146863

    Protein-protein interaction databases

    DIPiDIP-9931N.
    IntActiP28630. 49 interactions.
    MINTiMINT-1235044.
    STRINGi511145.b0640.

    Structurei

    Secondary structure

    1
    343
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 43
    Helixi6 – 83
    Helixi9 – 157
    Beta strandi19 – 268
    Helixi28 – 4417
    Beta strandi49 – 513
    Helixi61 – 699
    Beta strandi73 – 764
    Beta strandi78 – 836
    Helixi93 – 10311
    Beta strandi106 – 1083
    Beta strandi110 – 1134
    Helixi121 – 1233
    Helixi125 – 1306
    Helixi131 – 1333
    Beta strandi135 – 1384
    Turni144 – 1463
    Helixi147 – 15610
    Turni157 – 1593
    Helixi164 – 17411
    Helixi178 – 19114
    Helixi199 – 2068
    Helixi214 – 2229
    Helixi226 – 23510
    Turni236 – 2405
    Turni243 – 2453
    Helixi246 – 26116
    Turni262 – 2665
    Turni269 – 2757
    Helixi280 – 2823
    Turni283 – 2853
    Helixi286 – 2927
    Helixi295 – 31420
    Helixi325 – 3317

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JQJX-ray2.90C/D1-343[»]
    1JQLX-ray2.50B1-140[»]
    1JR3X-ray2.70D1-343[»]
    1XXHX-ray3.45A/F1-343[»]
    1XXIX-ray4.10A/F1-343[»]
    3GLFX-ray3.39A/F1-343[»]
    3GLGX-ray3.25A/F1-343[»]
    3GLHX-ray3.89A/F/K1-343[»]
    3GLIX-ray3.50A/F1-343[»]
    ProteinModelPortaliP28630.
    SMRiP28630. Positions 1-338.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP28630.

    Family & Domainsi

    Phylogenomic databases

    eggNOGiCOG1466.
    HOGENOMiHOG000256204.
    KOiK02340.
    OMAiQHRVWQN.
    OrthoDBiEOG6BCSPJ.
    PhylomeDBiP28630.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR008921. DNA_pol3_clamp-load_cplx_C.
    IPR010372. DNA_pol3_delta.
    IPR005790. DNA_polIII_delta.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF06144. DNA_pol3_delta. 1 hit.
    [Graphical view]
    SUPFAMiSSF48019. SSF48019. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR01128. holA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P28630-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH    50
    HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL 100
    TGLLHDDLLL IVRGNKLSKA QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW 150
    VAARAKQLNL ELDDAANQVL CYCYEGNLLA LAQALERLSL LWPDGKLTLP 200
    RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG SEPVILLRTL 250
    QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ 300
    AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG 343
    Length:343
    Mass (Da):38,704
    Last modified:December 1, 1992 - v1
    Checksum:i87239A678FE16BE2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L04576 Genomic DNA. Translation: AAA23675.1.
    M94267 Genomic DNA. Translation: AAB59047.1.
    U82598 Genomic DNA. Translation: AAB40841.1.
    U00096 Genomic DNA. Translation: AAC73741.1.
    AP009048 Genomic DNA. Translation: BAA35287.1.
    M18277 Genomic DNA. No translation available.
    PIRiA45251.
    RefSeqiNP_415173.1. NC_000913.3.
    YP_488931.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73741; AAC73741; b0640.
    BAA35287; BAA35287; BAA35287.
    GeneIDi12930914.
    947573.
    KEGGiecj:Y75_p0630.
    eco:b0640.
    PATRICi32116463. VBIEscCol129921_0671.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L04576 Genomic DNA. Translation: AAA23675.1 .
    M94267 Genomic DNA. Translation: AAB59047.1 .
    U82598 Genomic DNA. Translation: AAB40841.1 .
    U00096 Genomic DNA. Translation: AAC73741.1 .
    AP009048 Genomic DNA. Translation: BAA35287.1 .
    M18277 Genomic DNA. No translation available.
    PIRi A45251.
    RefSeqi NP_415173.1. NC_000913.3.
    YP_488931.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1JQJ X-ray 2.90 C/D 1-343 [» ]
    1JQL X-ray 2.50 B 1-140 [» ]
    1JR3 X-ray 2.70 D 1-343 [» ]
    1XXH X-ray 3.45 A/F 1-343 [» ]
    1XXI X-ray 4.10 A/F 1-343 [» ]
    3GLF X-ray 3.39 A/F 1-343 [» ]
    3GLG X-ray 3.25 A/F 1-343 [» ]
    3GLH X-ray 3.89 A/F/K 1-343 [» ]
    3GLI X-ray 3.50 A/F 1-343 [» ]
    ProteinModelPortali P28630.
    SMRi P28630. Positions 1-338.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9931N.
    IntActi P28630. 49 interactions.
    MINTi MINT-1235044.
    STRINGi 511145.b0640.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73741 ; AAC73741 ; b0640 .
    BAA35287 ; BAA35287 ; BAA35287 .
    GeneIDi 12930914.
    947573.
    KEGGi ecj:Y75_p0630.
    eco:b0640.
    PATRICi 32116463. VBIEscCol129921_0671.

    Organism-specific databases

    EchoBASEi EB1384.
    EcoGenei EG11412. holA.

    Phylogenomic databases

    eggNOGi COG1466.
    HOGENOMi HOG000256204.
    KOi K02340.
    OMAi QHRVWQN.
    OrthoDBi EOG6BCSPJ.
    PhylomeDBi P28630.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11412-MONOMER.
    ECOL316407:JW0635-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P28630.
    PROi P28630.

    Gene expression databases

    Genevestigatori P28630.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    InterProi IPR008921. DNA_pol3_clamp-load_cplx_C.
    IPR010372. DNA_pol3_delta.
    IPR005790. DNA_polIII_delta.
    IPR027417. P-loop_NTPase.
    [Graphical view ]
    Pfami PF06144. DNA_pol3_delta. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48019. SSF48019. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR01128. holA. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'."
      Dong Z., Onrust R., Skangalis M., O'Donnell M.
      J. Biol. Chem. 268:11758-11765(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Molecular cloning, sequencing, and overexpression of the structural gene encoding the delta subunit of Escherichia coli DNA polymerase III holoenzyme."
      Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.
      J. Bacteriol. 174:7013-7025(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome."
      Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S., Matsuzawa H., Ohta T., Matsuhashi M.
      J. Bacteriol. 169:5692-5699(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49.
      Strain: K12.
    8. "DNA polymerase III accessory proteins. II. Characterization of delta and delta'."
      Onrust R., O'Donnell M.
      J. Biol. Chem. 268:11766-11772(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    9. "Accessory protein function in the DNA polymerase III holoenzyme from E. coli."
      O'Donnell M.
      Bioessays 14:105-111(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    10. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.

    Entry informationi

    Entry nameiHOLA_ECOLI
    AccessioniPrimary (citable) accession number: P28630
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: December 1, 1992
    Last modified: July 9, 2014
    This is version 130 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references

    External Data

    Dasty 3