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P28631

- HOLB_ECOLI

UniProt

P28631 - HOLB_ECOLI

Protein

DNA polymerase III subunit delta'

Gene

holB

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 135 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      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.

    Catalytic activityi

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

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: InterPro
    2. DNA binding Source: InterPro
    3. DNA-directed DNA polymerase activity Source: UniProtKB-KW
    4. 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:EG11500-MONOMER.
    ECOL316407:JW1085-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase III subunit delta' (EC:2.7.7.7)
    Gene namesi
    Name:holB
    Ordered Locus Names:b1099, JW1085
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11500. holB.

    Subcellular locationi

    GO - Cellular componenti

    1. DNA polymerase III complex Source: EcoCyc

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 334334DNA polymerase III subunit delta'PRO_0000105513Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriP28631.

    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
    dnaXP0671017EBI-549161,EBI-549140
    dnaXP06710-16EBI-549161,EBI-6464728
    holAP2863017EBI-549161,EBI-549153
    holCP289055EBI-549161,EBI-549169
    mutLP233672EBI-549161,EBI-554913

    Protein-protein interaction databases

    DIPiDIP-9932N.
    IntActiP28631. 25 interactions.
    MINTiMINT-1239429.
    STRINGi511145.b1099.

    Structurei

    Secondary structure

    1
    334
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 73
    Helixi8 – 1912
    Beta strandi25 – 306
    Helixi37 – 4812
    Beta strandi55 – 573
    Helixi63 – 708
    Beta strandi76 – 794
    Beta strandi86 – 883
    Helixi90 – 9910
    Beta strandi110 – 1156
    Helixi117 – 1193
    Helixi122 – 13211
    Beta strandi139 – 1468
    Helixi148 – 1503
    Helixi153 – 1564
    Beta strandi159 – 1635
    Helixi169 – 17911
    Helixi184 – 19310
    Turni194 – 1963
    Helixi198 – 2036
    Helixi208 – 22619
    Helixi230 – 2323
    Helixi233 – 2364
    Helixi241 – 25515
    Turni259 – 2613
    Helixi271 – 28010
    Helixi283 – 30321
    Helixi308 – 32215
    Beta strandi324 – 3263

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A5TX-ray2.20A1-334[»]
    1JR3X-ray2.70E1-334[»]
    1XXHX-ray3.45E/J1-334[»]
    1XXIX-ray4.10E/J1-334[»]
    3GLFX-ray3.39E/J1-334[»]
    3GLGX-ray3.25E/J1-334[»]
    3GLHX-ray3.89E/J/O1-334[»]
    3GLIX-ray3.50E/J1-334[»]
    ProteinModelPortaliP28631.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP28631.

    Family & Domainsi

    Phylogenomic databases

    eggNOGiCOG0470.
    HOGENOMiHOG000192595.
    KOiK02341.
    OMAiCHSCHLM.
    OrthoDBiEOG6W9X5M.
    PhylomeDBiP28631.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR008921. DNA_pol3_clamp-load_cplx_C.
    IPR004622. DNA_pol_HolB.
    IPR015199. DNA_pol_III_delta_C.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF09115. DNApol3-delta_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF48019. SSF48019. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00678. holB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P28631-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC    50
    QQPQGHKSCG HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL 100
    NEHARLGGAK VVWVTDAALL TDAAANALLK TLEEPPAETW FFLATREPER 150
    LLATLRSRCR LHYLAPPPEQ YAVTWLSREV TMSQDALLAA LRLSAGSPGA 200
    ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ APARLHWLAT 250
    LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL 300
    MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL 334
    Length:334
    Mass (Da):36,937
    Last modified:November 1, 1997 - v2
    Checksum:iDC9DAA644AD8A096
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti166 – 1661P → G in AAA23708. (PubMed:8505303)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L04577 Genomic DNA. Translation: AAA23708.1.
    L01483 Genomic DNA. Translation: AAA23696.1.
    U00096 Genomic DNA. Translation: AAC74183.1.
    AP009048 Genomic DNA. Translation: BAA35906.1.
    PIRiS35523.
    RefSeqiNP_415617.1. NC_000913.3.
    YP_489367.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74183; AAC74183; b1099.
    BAA35906; BAA35906; BAA35906.
    GeneIDi12934122.
    945661.
    KEGGiecj:Y75_p1069.
    eco:b1099.
    PATRICi32117439. VBIEscCol129921_1142.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L04577 Genomic DNA. Translation: AAA23708.1 .
    L01483 Genomic DNA. Translation: AAA23696.1 .
    U00096 Genomic DNA. Translation: AAC74183.1 .
    AP009048 Genomic DNA. Translation: BAA35906.1 .
    PIRi S35523.
    RefSeqi NP_415617.1. NC_000913.3.
    YP_489367.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1A5T X-ray 2.20 A 1-334 [» ]
    1JR3 X-ray 2.70 E 1-334 [» ]
    1XXH X-ray 3.45 E/J 1-334 [» ]
    1XXI X-ray 4.10 E/J 1-334 [» ]
    3GLF X-ray 3.39 E/J 1-334 [» ]
    3GLG X-ray 3.25 E/J 1-334 [» ]
    3GLH X-ray 3.89 E/J/O 1-334 [» ]
    3GLI X-ray 3.50 E/J 1-334 [» ]
    ProteinModelPortali P28631.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9932N.
    IntActi P28631. 25 interactions.
    MINTi MINT-1239429.
    STRINGi 511145.b1099.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74183 ; AAC74183 ; b1099 .
    BAA35906 ; BAA35906 ; BAA35906 .
    GeneIDi 12934122.
    945661.
    KEGGi ecj:Y75_p1069.
    eco:b1099.
    PATRICi 32117439. VBIEscCol129921_1142.

    Organism-specific databases

    EchoBASEi EB1463.
    EcoGenei EG11500. holB.

    Phylogenomic databases

    eggNOGi COG0470.
    HOGENOMi HOG000192595.
    KOi K02341.
    OMAi CHSCHLM.
    OrthoDBi EOG6W9X5M.
    PhylomeDBi P28631.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11500-MONOMER.
    ECOL316407:JW1085-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P28631.
    PROi P28631.

    Gene expression databases

    Genevestigatori P28631.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    InterProi IPR008921. DNA_pol3_clamp-load_cplx_C.
    IPR004622. DNA_pol_HolB.
    IPR015199. DNA_pol_III_delta_C.
    IPR027417. P-loop_NTPase.
    [Graphical view ]
    Pfami PF09115. DNApol3-delta_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48019. SSF48019. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR00678. holB. 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. "Identification, isolation, and characterization 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. 175:3812-3822(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "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.
    6. "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.
    7. "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.
    8. "Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III."
      Guenther B., Onrust R., Sali A., O'Donnell M., Kuriyan J.
      Cell 91:335-345(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).

    Entry informationi

    Entry nameiHOLB_ECOLI
    AccessioniPrimary (citable) accession number: P28631
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 135 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, 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