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P28632

- HOLD_ECOLI

UniProt

P28632 - HOLD_ECOLI

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Protein
DNA polymerase III subunit psi
Gene
holD, b4372, JW4334
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

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 exact function of the psi subunit is unknown.

Catalytic activityi

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

GO - Molecular functioni

  1. 3'-5' exonuclease activity Source: InterPro
  2. DNA-directed DNA polymerase activity Source: UniProtKB-KW
  3. protein binding Source: IntAct
Complete GO annotation...

GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA replication

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11414-MONOMER.
    ECOL316407:JW4334-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase III subunit psi (EC:2.7.7.7)
    Gene namesi
    Name:holD
    Ordered Locus Names:b4372, JW4334
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11414. holD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 137137DNA polymerase III subunit psi
    PRO_0000105520Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriP28632.

    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
    dnaXP0671018EBI-549176,EBI-549140
    holCP2890522EBI-549176,EBI-549169

    Protein-protein interaction databases

    DIPiDIP-9934N.
    IntActiP28632. 22 interactions.
    MINTiMINT-1224283.
    STRINGi511145.b4372.

    Structurei

    Secondary structure

    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 129
    Beta strandi16 – 205
    Helixi22 – 243
    Beta strandi39 – 424
    Helixi52 – 6110
    Helixi65 – 673
    Beta strandi68 – 714
    Helixi73 – 764
    Beta strandi87 – 915
    Beta strandi97 – 1004
    Beta strandi102 – 1054
    Helixi108 – 1136
    Helixi115 – 12713
    Helixi129 – 1324

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EM8X-ray2.10B/D26-137[»]
    3GLIX-ray3.50O/P2-28[»]
    3SXUX-ray1.85B2-137[»]
    ProteinModelPortaliP28632.
    SMRiP28632. Positions 2-137.

    Miscellaneous databases

    EvolutionaryTraceiP28632.

    Family & Domainsi

    Phylogenomic databases

    eggNOGiCOG3050.
    HOGENOMiHOG000218328.
    KOiK02344.
    OMAiITQWTLR.
    OrthoDBiEOG6WDSJJ.

    Family and domain databases

    Gene3Di3.40.50.10220. 1 hit.
    InterProiIPR004615. DNA_pol_III_psi.
    IPR018382. DNA_pol_III_psi_subgr.
    [Graphical view]
    PfamiPF03603. DNA_III_psi. 1 hit.
    [Graphical view]
    PIRSFiPIRSF029225. DNA_pol_III_psi. 1 hit.
    ProDomiPD032475. DNA_pol_III_psi. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SUPFAMiSSF102220. SSF102220. 1 hit.
    TIGRFAMsiTIGR00664. DNA_III_psi. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P28632-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTSRRDWQLQ QLGITQWSLR RPGALQGEIA IAIPAHVRLV MVANDLPALT    50
    DPLVSDVLRA LTVSPDQVLQ LTPEKIAMLP QGSHCNSWRL GTDEPLSLEG 100
    AQVASPALTD LRANPTARAA LWQQICTYEH DFFPRND 137
    Length:137
    Mass (Da):15,174
    Last modified:December 1, 1992 - v1
    Checksum:i5B7356201E7E27FE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L04575 Genomic DNA. Translation: AAA24435.1.
    L05387 Unassigned DNA. Translation: AAA03076.1.
    X06117 Genomic DNA. No translation available.
    U14003 Genomic DNA. Translation: AAA97268.1.
    U00096 Genomic DNA. Translation: AAC77325.1.
    AP009048 Genomic DNA. Translation: BAE78360.1.
    PIRiA48647.
    RefSeqiNP_418789.1. NC_000913.3.
    YP_492501.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77325; AAC77325; b4372.
    BAE78360; BAE78360; BAE78360.
    GeneIDi12933791.
    948890.
    KEGGiecj:Y75_p4255.
    eco:b4372.
    PATRICi32124354. VBIEscCol129921_4517.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L04575 Genomic DNA. Translation: AAA24435.1 .
    L05387 Unassigned DNA. Translation: AAA03076.1 .
    X06117 Genomic DNA. No translation available.
    U14003 Genomic DNA. Translation: AAA97268.1 .
    U00096 Genomic DNA. Translation: AAC77325.1 .
    AP009048 Genomic DNA. Translation: BAE78360.1 .
    PIRi A48647.
    RefSeqi NP_418789.1. NC_000913.3.
    YP_492501.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EM8 X-ray 2.10 B/D 26-137 [» ]
    3GLI X-ray 3.50 O/P 2-28 [» ]
    3SXU X-ray 1.85 B 2-137 [» ]
    ProteinModelPortali P28632.
    SMRi P28632. Positions 2-137.
    ModBasei Search...

    Protein-protein interaction databases

    DIPi DIP-9934N.
    IntActi P28632. 22 interactions.
    MINTi MINT-1224283.
    STRINGi 511145.b4372.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC77325 ; AAC77325 ; b4372 .
    BAE78360 ; BAE78360 ; BAE78360 .
    GeneIDi 12933791.
    948890.
    KEGGi ecj:Y75_p4255.
    eco:b4372.
    PATRICi 32124354. VBIEscCol129921_4517.

    Organism-specific databases

    EchoBASEi EB1386.
    EcoGenei EG11414. holD.

    Phylogenomic databases

    eggNOGi COG3050.
    HOGENOMi HOG000218328.
    KOi K02344.
    OMAi ITQWTLR.
    OrthoDBi EOG6WDSJJ.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11414-MONOMER.
    ECOL316407:JW4334-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P28632.
    PROi P28632.

    Gene expression databases

    Genevestigatori P28632.

    Family and domain databases

    Gene3Di 3.40.50.10220. 1 hit.
    InterProi IPR004615. DNA_pol_III_psi.
    IPR018382. DNA_pol_III_psi_subgr.
    [Graphical view ]
    Pfami PF03603. DNA_III_psi. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF029225. DNA_pol_III_psi. 1 hit.
    ProDomi PD032475. DNA_pol_III_psi. 1 hit.
    [Graphical view ] [Entries sharing at least one domain ]
    SUPFAMi SSF102220. SSF102220. 1 hit.
    TIGRFAMsi TIGR00664. DNA_III_psi. 1 hit.
    ProtoNeti Search...

    Publicationsi

    « Hide 'large scale' publications
    1. "DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi."
      Xiao H., Crombie R., Dong Z., Onrust R., O'Donnell M.
      J. Biol. Chem. 268:11773-11778(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Identification, isolation, and overexpression of the gene encoding the psi subunit of DNA polymerase III holoenzyme."
      Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.
      J. Bacteriol. 175:5604-5610(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12."
      Yoshikawa A., Isono S., Sheback A., Isono K.
      Mol. Gen. Genet. 209:481-488(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    4. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      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. "DNA polymerase III accessory proteins. IV. Characterization of chi and psi."
      Xiao H., Dong Z., O'Donnell M.
      J. Biol. Chem. 268:11779-11784(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    8. "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.
    9. "Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex."
      Gulbis J.M., Kazmirski S.L., Finkelstein J., Kelman Z., O'Donnell M., Kuriyan J.
      Eur. J. Biochem. 271:439-449(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 26-137.

    Entry informationi

    Entry nameiHOLD_ECOLI
    AccessioniPrimary (citable) accession number: P28632
    Secondary accession number(s): Q2M5U6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: December 1, 1992
    Last modified: June 11, 2014
    This is version 120 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, 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

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