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P0ABS5

- DNAG_ECOLI

UniProt

P0ABS5 - DNAG_ECOLI

Protein

DNA primase

Gene

dnaG

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 1 (21 Jul 1986)
      Previous versions | rss
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    Functioni

    RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.2 PublicationsUniRule annotation

    Cofactori

    Binds 1 zinc ion per monomer.2 PublicationsUniRule annotation
    Magnesium. Binds two Mg2+ per subunit.UniRule annotation

    Enzyme regulationi

    Activity can be regulated by an intermolecular trans association between the zinc-binding domain and the catalytic core domain of two different primase molecules.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi265 – 2651Magnesium 1; catalyticUniRule annotation
    Metal bindingi309 – 3091Magnesium 1; catalyticUniRule annotation
    Metal bindingi309 – 3091Magnesium 2UniRule annotation
    Metal bindingi311 – 3111Magnesium 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri40 – 6425CHC2-typeUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA primase activity Source: EcoliWiki
    3. protein binding Source: IntAct
    4. zinc ion binding Source: EcoliWiki

    GO - Biological processi

    1. DNA replication, synthesis of RNA primer Source: EcoliWiki

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA replication, Transcription

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10239-MONOMER.
    ECOL316407:JW3038-MONOMER.
    MetaCyc:EG10239-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA primaseUniRule annotation (EC:2.7.7.-UniRule annotation)
    Gene namesi
    Name:dnaGUniRule annotation
    Synonyms:dnaP, parB
    Ordered Locus Names:b3066, JW3038
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10239. dnaG.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki
    2. primosome complex Source: UniProtKB-KW

    Keywords - Cellular componenti

    DNA-directed RNA polymerase, Primosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi165 – 1651W → A: Abolishes DNA-binding and primer synthesis. 1 Publication
    Mutagenesisi199 – 1991R → A: Abolishes primer synthesis but can still bind DNA. Abolishes DNA-binding; when associated with A-201. 1 Publication
    Mutagenesisi201 – 2011R → A: Abolishes primer synthesis but can still bind DNA. Abolishes DNA-binding; when associated with A-199. 1 Publication
    Mutagenesisi576 – 5761Q → A: Decreases interaction with DnaB and primase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 581581DNA primasePRO_0000180490Add
    BLAST

    Proteomic databases

    PaxDbiP0ABS5.
    PRIDEiP0ABS5.

    Expressioni

    Gene expression databases

    GenevestigatoriP0ABS5.

    Interactioni

    Subunit structurei

    Monomer. Interacts with DnaB. The primase-helicase complex is composed of up to three DnaG bound to one DnaB hexamer.6 PublicationsUniRule annotation

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    dnaBP0ACB03EBI-549259,EBI-548978
    ssbP0AGE02EBI-549259,EBI-1118620

    Protein-protein interaction databases

    DIPiDIP-47954N.
    IntActiP0ABS5. 17 interactions.
    MINTiMINT-1222307.
    STRINGi511145.b3066.

    Structurei

    Secondary structure

    1
    581
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi116 – 13116
    Helixi134 – 1363
    Helixi137 – 1459
    Helixi150 – 1567
    Beta strandi159 – 1613
    Beta strandi163 – 1653
    Helixi167 – 1726
    Helixi176 – 1849
    Beta strandi187 – 1904
    Beta strandi196 – 1994
    Beta strandi202 – 2098
    Beta strandi211 – 2133
    Beta strandi215 – 22511
    Beta strandi229 – 2324
    Turni241 – 2433
    Helixi248 – 2536
    Beta strandi261 – 2666
    Helixi267 – 2759
    Beta strandi281 – 2833
    Beta strandi285 – 2884
    Helixi291 – 30010
    Beta strandi302 – 31110
    Helixi312 – 32514
    Helixi326 – 3283
    Beta strandi334 – 3407
    Helixi346 – 36217
    Helixi368 – 3769
    Helixi377 – 3793
    Helixi385 – 39915
    Helixi405 – 41915
    Helixi424 – 4274
    Helixi448 – 46013
    Helixi462 – 4676
    Turni472 – 4743
    Helixi476 – 4783
    Helixi482 – 49312
    Helixi500 – 5056
    Turni507 – 5093
    Helixi510 – 5123
    Helixi513 – 54028
    Turni541 – 5433
    Helixi544 – 55815
    Turni559 – 5613
    Helixi565 – 57713

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DD9X-ray1.60A111-433[»]
    1DDEX-ray1.70A111-433[»]
    1EQNX-ray2.90A/B/C/D/E111-429[»]
    1T3WX-ray2.80A/B434-581[»]
    2HAJNMR-A434-581[»]
    3B39X-ray2.35A/B111-429[»]
    ProteinModelPortaliP0ABS5.
    SMRiP0ABS5. Positions 4-418, 447-581.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0ABS5.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini259 – 34183ToprimUniRule annotationAdd
    BLAST

    Domaini

    Contains an N-terminal zinc-binding domain, a central core domain that contains the primase activity, and a C-terminal DnaB-binding domain.3 PublicationsUniRule annotation

    Sequence similaritiesi

    Belongs to the DnaG primase family.UniRule annotation
    Contains 1 Toprim domain.UniRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri40 – 6425CHC2-typeUniRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0358.
    HOGENOMiHOG000014483.
    KOiK02316.
    OMAiVMDHDQL.
    OrthoDBiEOG6XDGTR.
    PhylomeDBiP0ABS5.

    Family and domain databases

    Gene3Di1.10.860.10. 1 hit.
    3.90.580.10. 1 hit.
    3.90.980.10. 1 hit.
    HAMAPiMF_00974. DNA_primase_DnaG.
    InterProiIPR016136. DNA_helicase_N/primase_C.
    IPR013264. DNA_primase_core_N.
    IPR019475. DNA_primase_DnaB-bd.
    IPR006295. DNA_primase_DnaG.
    IPR013173. DNA_primase_DnaG_DnaB-bd_dom.
    IPR006171. Toprim_domain.
    IPR002694. Znf_CHC2.
    [Graphical view]
    PfamiPF10410. DnaB_bind. 1 hit.
    PF08278. DnaG_DnaB_bind. 1 hit.
    PF13662. Toprim_4. 1 hit.
    PF08275. Toprim_N. 1 hit.
    PF01807. zf-CHC2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF002811. DnaG. 1 hit.
    SMARTiSM00766. DnaG_DnaB_bind. 1 hit.
    SM00493. TOPRIM. 1 hit.
    SM00400. ZnF_CHCC. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01391. dnaG. 1 hit.
    PROSITEiPS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0ABS5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAGRIPRVFI NDLLARTDIV DLIDARVKLK KQGKNFHACC PFHNEKTPSF    50
    TVNGEKQFYH CFGCGAHGNA IDFLMNYDKL EFVETVEELA AMHNLEVPFE 100
    AGSGPSQIER HQRQTLYQLM DGLNTFYQQS LQQPVATSAR QYLEKRGLSH 150
    EVIARFAIGF APPGWDNVLK RFGGNPENRQ SLIDAGMLVT NDQGRSYDRF 200
    RERVMFPIRD KRGRVIGFGG RVLGNDTPKY LNSPETDIFH KGRQLYGLYE 250
    AQQDNAEPNR LLVVEGYMDV VALAQYGINY AVASLGTSTT ADHIQLLFRA 300
    TNNVICCYDG DRAGRDAAWR ALETALPYMT DGRQLRFMFL PDGEDPDTLV 350
    RKEGKEAFEA RMEQAMPLSA FLFNSLMPQV DLSTPDGRAR LSTLALPLIS 400
    QVPGETLRIY LRQELGNKLG ILDDSQLERL MPKAAESGVS RPVPQLKRTT 450
    MRILIGLLVQ NPELATLVPP LENLDENKLP GLGLFRELVN TCLSQPGLTT 500
    GQLLEHYRGT NNAATLEKLS MWDDIADKNI AEQTFTDSLN HMFDSLLELR 550
    QEELIARERT HGLSNEERLE LWTLNQELAK K 581
    Length:581
    Mass (Da):65,565
    Last modified:July 21, 1986 - v1
    Checksum:i294CF020E7B45D94
    GO

    Sequence cautioni

    The sequence CAA23531.1 differs from that shown. Reason: Frameshift at positions 106 and 169.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti24 – 241D → N in CAA23636. (PubMed:6222240)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01687 Genomic DNA. Translation: AAA24600.1.
    V00274 Genomic DNA. Translation: CAA23531.1. Frameshift.
    U28379 Genomic DNA. Translation: AAA89146.1.
    U00096 Genomic DNA. Translation: AAC76102.1.
    AP009048 Genomic DNA. Translation: BAE77117.1.
    V00346 Genomic DNA. Translation: CAA23636.1.
    PIRiA03423. RYEC2.
    RefSeqiNP_417538.1. NC_000913.3.
    YP_491258.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76102; AAC76102; b3066.
    BAE77117; BAE77117; BAE77117.
    GeneIDi12933152.
    947570.
    KEGGiecj:Y75_p2992.
    eco:b3066.
    PATRICi32121546. VBIEscCol129921_3160.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01687 Genomic DNA. Translation: AAA24600.1 .
    V00274 Genomic DNA. Translation: CAA23531.1 . Frameshift.
    U28379 Genomic DNA. Translation: AAA89146.1 .
    U00096 Genomic DNA. Translation: AAC76102.1 .
    AP009048 Genomic DNA. Translation: BAE77117.1 .
    V00346 Genomic DNA. Translation: CAA23636.1 .
    PIRi A03423. RYEC2.
    RefSeqi NP_417538.1. NC_000913.3.
    YP_491258.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DD9 X-ray 1.60 A 111-433 [» ]
    1DDE X-ray 1.70 A 111-433 [» ]
    1EQN X-ray 2.90 A/B/C/D/E 111-429 [» ]
    1T3W X-ray 2.80 A/B 434-581 [» ]
    2HAJ NMR - A 434-581 [» ]
    3B39 X-ray 2.35 A/B 111-429 [» ]
    ProteinModelPortali P0ABS5.
    SMRi P0ABS5. Positions 4-418, 447-581.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-47954N.
    IntActi P0ABS5. 17 interactions.
    MINTi MINT-1222307.
    STRINGi 511145.b3066.

    Proteomic databases

    PaxDbi P0ABS5.
    PRIDEi P0ABS5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76102 ; AAC76102 ; b3066 .
    BAE77117 ; BAE77117 ; BAE77117 .
    GeneIDi 12933152.
    947570.
    KEGGi ecj:Y75_p2992.
    eco:b3066.
    PATRICi 32121546. VBIEscCol129921_3160.

    Organism-specific databases

    EchoBASEi EB0235.
    EcoGenei EG10239. dnaG.

    Phylogenomic databases

    eggNOGi COG0358.
    HOGENOMi HOG000014483.
    KOi K02316.
    OMAi VMDHDQL.
    OrthoDBi EOG6XDGTR.
    PhylomeDBi P0ABS5.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10239-MONOMER.
    ECOL316407:JW3038-MONOMER.
    MetaCyc:EG10239-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0ABS5.
    PROi P0ABS5.

    Gene expression databases

    Genevestigatori P0ABS5.

    Family and domain databases

    Gene3Di 1.10.860.10. 1 hit.
    3.90.580.10. 1 hit.
    3.90.980.10. 1 hit.
    HAMAPi MF_00974. DNA_primase_DnaG.
    InterProi IPR016136. DNA_helicase_N/primase_C.
    IPR013264. DNA_primase_core_N.
    IPR019475. DNA_primase_DnaB-bd.
    IPR006295. DNA_primase_DnaG.
    IPR013173. DNA_primase_DnaG_DnaB-bd_dom.
    IPR006171. Toprim_domain.
    IPR002694. Znf_CHC2.
    [Graphical view ]
    Pfami PF10410. DnaB_bind. 1 hit.
    PF08278. DnaG_DnaB_bind. 1 hit.
    PF13662. Toprim_4. 1 hit.
    PF08275. Toprim_N. 1 hit.
    PF01807. zf-CHC2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF002811. DnaG. 1 hit.
    SMARTi SM00766. DnaG_DnaB_bind. 1 hit.
    SM00493. TOPRIM. 1 hit.
    SM00400. ZnF_CHCC. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01391. dnaG. 1 hit.
    PROSITEi PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12."
      Burton Z.F., Gross C.A., Watanabe K.K., Burgess R.R.
      Cell 32:335-349(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequences of the Escherichia coli dnaG primase gene and regulation of its expression."
      Smiley B.L., Lupski J.R., Svec P.S., McMacken R., Godson G.N.
      Proc. Natl. Acad. Sci. U.S.A. 79:4550-4554(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12."
      Lupski J.R., Smiley B.L., Godson G.N.
      Mol. Gen. Genet. 189:48-57(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-81.
      Strain: K12.
    6. "Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains."
      Rowen L., Kornberg A.
      J. Biol. Chem. 253:758-764(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    7. "Enriched sources of Escherichia coli replication proteins. The dnaG primase is a zinc metalloprotein."
      Stamford N.P.J., Lilley P.E., Dixon N.E.
      Biochim. Biophys. Acta 1132:17-25(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, SUBUNIT, ZINC-BINDING.
    8. "The role of zinc and the reactivity of cysteines in Escherichia coli primase."
      Griep M.A., Lokey E.R.
      Biochemistry 35:8260-8267(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, ZINC-BINDING.
    9. "Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA."
      Lu Y.B., Ratnakar P.V., Mohanty B.K., Bastia D.
      Proc. Natl. Acad. Sci. U.S.A. 93:12902-12907(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH DNAB, MUTAGENESIS OF GLN-576.
    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.
    11. "Mechanism and stoichiometry of interaction of DnaG primase with DnaB helicase of Escherichia coli in RNA primer synthesis."
      Mitkova A.V., Khopde S.M., Biswas S.B.
      J. Biol. Chem. 278:52253-52261(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, INTERACTION WITH DNAB.
    12. "Crosstalk between primase subunits can act to regulate primer synthesis in trans."
      Corn J.E., Pease P.J., Hura G.L., Berger J.M.
      Mol. Cell 20:391-401(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION.
    13. "A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases."
      Podobnik M., McInerney P., O'Donnell M., Kuriyan J.
      J. Mol. Biol. 300:353-362(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 109-429.
    14. "Structure of the RNA polymerase domain of E. coli primase."
      Keck J.L., Roche D.D., Lynch A.S., Berger J.M.
      Science 287:2482-2486(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 111-433, DOMAIN.
    15. "Crystal and solution structures of the helicase-binding domain of Escherichia coli primase."
      Oakley A.J., Loscha K.V., Schaeffer P.M., Liepinsh E., Pintacuda G., Wilce M.C., Otting G., Dixon N.E.
      J. Biol. Chem. 280:11495-11504(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 434-581, INTERACTION WITH DNAB, DOMAIN.
    16. "Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase."
      Su X.C., Schaeffer P.M., Loscha K.V., Gan P.H., Dixon N.E., Otting G.
      FEBS J. 273:4997-5009(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 434-581, SUBUNIT, DOMAIN.
    17. "Identification of a DNA primase template tracking site redefines the geometry of primer synthesis."
      Corn J.E., Pelton J.G., Berger J.M.
      Nat. Struct. Mol. Biol. 15:163-169(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 111-429, DNA-BINDING, MUTAGENESIS OF TRP-165; ARG-199 AND ARG-201.

    Entry informationi

    Entry nameiDNAG_ECOLI
    AccessioniPrimary (citable) accession number: P0ABS5
    Secondary accession number(s): P02922
    , P02923, Q2M9D9, Q47613
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: October 1, 2014
    This is version 89 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
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3