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P03004

- DNAA_ECOLI

UniProt

P03004 - DNAA_ECOLI

Protein

Chromosomal replication initiator protein DnaA

Gene

dnaA

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 144 (01 Oct 2014)
      Sequence version 2 (01 Jul 1993)
      Previous versions | rss
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    Functioni

    Plays a key role in the initiation and regulation of chromosomal replication. Binds in an ATP-dependent fashion to the origin of replication (oriC) to initiate formation of the DNA replication initiation complex exactly once per cell cycle. Binds the DnaA box (consensus sequence 5'-TTATC[CA]A[CA]A-3'); subsequent binding of DNA polymerase III subunits leads to replisome formation. The DnaA-ATP form converts to DnaA-ADP; once converted to ADP the protein cannot initiate replication, ensuring only 1 round of replication per cell cycle. DnaA can inhibit its own gene expression as well as that of other genes such as dam, rpoH, ftsA and mioC.
    Also required for replication of plasmid DNA; binds 4 dnaA boxes in the minimal plasmid RK2 replication origin (oriV).

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi172 – 1798ATPCurated

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. DNA binding Source: EcoCyc
    3. DNA replication origin binding Source: EcoCyc
    4. nucleoside-triphosphatase activity Source: InterPro
    5. protein binding Source: IntAct
    6. sequence-specific DNA binding Source: EcoliWiki

    GO - Biological processi

    1. DNA replication Source: EcoliWiki
    2. DNA replication initiation Source: UniProtKB-HAMAP
    3. negative regulation of DNA replication Source: UniProtKB-KW
    4. regulation of DNA replication Source: EcoliWiki
    5. regulation of transcription, DNA-templated Source: UniProtKB-KW
    6. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    DNA replication inhibitor, Repressor

    Keywords - Biological processi

    DNA replication, Transcription, Transcription regulation

    Keywords - Ligandi

    ATP-binding, DNA-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:PD03831.
    ECOL316407:JW3679-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Chromosomal replication initiator protein DnaA
    Gene namesi
    Name:dnaA
    Ordered Locus Names:b3702, JW3679
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10235. dnaA.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. plasma membrane Source: EcoCyc

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 467467Chromosomal replication initiator protein DnaAPRO_0000114174Add
    BLAST

    Proteomic databases

    PaxDbiP03004.
    PRIDEiP03004.

    Expressioni

    Gene expression databases

    GenevestigatoriP03004.

    Interactioni

    Subunit structurei

    Some 20 DnaA protein molecules bind their sites in oriC. Forms the RIDA (regulatory inactivation of DnaA) complex with ATP-DnaA, ADP-Hda and the DNA-loaded sliding beta clamp (dnaN). Interacts with DiaA; this stimulates the association of DnaA with the origin of replication.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    diaAP668175EBI-548951,EBI-1125806
    dnaBP0ACB04EBI-548951,EBI-548978
    dpsP0ABT22EBI-548951,EBI-549640
    hdaP699312EBI-548951,EBI-545453
    hupAP0ACF05EBI-548951,EBI-547648
    rplBP604224EBI-548951,EBI-543515

    Protein-protein interaction databases

    DIPiDIP-9455N.
    IntActiP03004. 44 interactions.
    MINTiMINT-207293.
    STRINGi511145.b3702.

    Structurei

    Secondary structure

    1
    467
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 1612
    Helixi21 – 244
    Turni25 – 284
    Beta strandi29 – 335
    Beta strandi35 – 4410
    Helixi45 – 539
    Helixi55 – 6612
    Beta strandi68 – 703
    Beta strandi77 – 804
    Helixi376 – 38611
    Helixi391 – 3955
    Helixi401 – 41717
    Helixi422 – 4287
    Helixi434 – 45017
    Helixi452 – 46514

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J1VX-ray2.10A374-467[»]
    2E0GNMR-A2-108[»]
    ProteinModelPortaliP03004.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP03004.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DnaA family.Curated

    Phylogenomic databases

    eggNOGiCOG0593.
    HOGENOMiHOG000235659.
    KOiK02313.
    OMAiNRTFTFD.
    OrthoDBiEOG689HR1.
    PhylomeDBiP03004.

    Family and domain databases

    Gene3Di1.10.1750.10. 1 hit.
    3.40.50.300. 1 hit.
    HAMAPiMF_00377. DnaA_bact.
    InterProiIPR003593. AAA+_ATPase.
    IPR001957. Chromosome_initiator_DnaA.
    IPR020591. Chromosome_initiator_DnaA-like.
    IPR018312. Chromosome_initiator_DnaA_CS.
    IPR013159. DnaA_C.
    IPR013317. DnaA_Hda.
    IPR024633. DnaA_N_dom.
    IPR027417. P-loop_NTPase.
    IPR010921. Trp_repressor/repl_initiator.
    [Graphical view]
    PfamiPF00308. Bac_DnaA. 1 hit.
    PF08299. Bac_DnaA_C. 1 hit.
    PF11638. DnaA_N. 1 hit.
    [Graphical view]
    PRINTSiPR00051. DNAA.
    SMARTiSM00382. AAA. 1 hit.
    SM00760. Bac_DnaA_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF48295. SSF48295. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00362. DnaA. 1 hit.
    PROSITEiPS01008. DNAA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P03004-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLSLWQQCL ARLQDELPAT EFSMWIRPLQ AELSDNTLAL YAPNRFVLDW    50
    VRDKYLNNIN GLLTSFCGAD APQLRFEVGT KPVTQTPQAA VTSNVAAPAQ 100
    VAQTQPQRAA PSTRSGWDNV PAPAEPTYRS NVNVKHTFDN FVEGKSNQLA 150
    RAAARQVADN PGGAYNPLFL YGGTGLGKTH LLHAVGNGIM ARKPNAKVVY 200
    MHSERFVQDM VKALQNNAIE EFKRYYRSVD ALLIDDIQFF ANKERSQEEF 250
    FHTFNALLEG NQQIILTSDR YPKEINGVED RLKSRFGWGL TVAIEPPELE 300
    TRVAILMKKA DENDIRLPGE VAFFIAKRLR SNVRELEGAL NRVIANANFT 350
    GRAITIDFVR EALRDLLALQ EKLVTIDNIQ KTVAEYYKIK VADLLSKRRS 400
    RSVARPRQMA MALAKELTNH SLPEIGDAFG GRDHTTVLHA CRKIEQLREE 450
    SHDIKEDFSN LIRTLSS 467
    Length:467
    Mass (Da):52,551
    Last modified:July 1, 1993 - v2
    Checksum:i607C8366A8CDCCED
    GO

    Sequence cautioni

    The sequence AAA62053.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti69 – 702AD → RI(PubMed:6296774)Curated
    Sequence conflicti403 – 4075VARPR → GXGPG in AAA62053. (PubMed:7686882)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01602 Genomic DNA. Translation: AAB59149.1.
    X01861 Genomic DNA. Translation: CAA25980.1.
    L10328 Genomic DNA. Translation: AAA62053.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76725.1.
    AP009048 Genomic DNA. Translation: BAE77592.1.
    PIRiG65172. IQECDA.
    RefSeqiNP_418157.1. NC_000913.3.
    YP_491733.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76725; AAC76725; b3702.
    BAE77592; BAE77592; BAE77592.
    GeneIDi12932545.
    948217.
    KEGGiecj:Y75_p3471.
    eco:b3702.
    PATRICi32122901. VBIEscCol129921_3826.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01602 Genomic DNA. Translation: AAB59149.1 .
    X01861 Genomic DNA. Translation: CAA25980.1 .
    L10328 Genomic DNA. Translation: AAA62053.1 . Different initiation.
    U00096 Genomic DNA. Translation: AAC76725.1 .
    AP009048 Genomic DNA. Translation: BAE77592.1 .
    PIRi G65172. IQECDA.
    RefSeqi NP_418157.1. NC_000913.3.
    YP_491733.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1J1V X-ray 2.10 A 374-467 [» ]
    2E0G NMR - A 2-108 [» ]
    ProteinModelPortali P03004.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9455N.
    IntActi P03004. 44 interactions.
    MINTi MINT-207293.
    STRINGi 511145.b3702.

    Proteomic databases

    PaxDbi P03004.
    PRIDEi P03004.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76725 ; AAC76725 ; b3702 .
    BAE77592 ; BAE77592 ; BAE77592 .
    GeneIDi 12932545.
    948217.
    KEGGi ecj:Y75_p3471.
    eco:b3702.
    PATRICi 32122901. VBIEscCol129921_3826.

    Organism-specific databases

    EchoBASEi EB0231.
    EcoGenei EG10235. dnaA.

    Phylogenomic databases

    eggNOGi COG0593.
    HOGENOMi HOG000235659.
    KOi K02313.
    OMAi NRTFTFD.
    OrthoDBi EOG689HR1.
    PhylomeDBi P03004.

    Enzyme and pathway databases

    BioCyci EcoCyc:PD03831.
    ECOL316407:JW3679-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P03004.
    PROi P03004.

    Gene expression databases

    Genevestigatori P03004.

    Family and domain databases

    Gene3Di 1.10.1750.10. 1 hit.
    3.40.50.300. 1 hit.
    HAMAPi MF_00377. DnaA_bact.
    InterProi IPR003593. AAA+_ATPase.
    IPR001957. Chromosome_initiator_DnaA.
    IPR020591. Chromosome_initiator_DnaA-like.
    IPR018312. Chromosome_initiator_DnaA_CS.
    IPR013159. DnaA_C.
    IPR013317. DnaA_Hda.
    IPR024633. DnaA_N_dom.
    IPR027417. P-loop_NTPase.
    IPR010921. Trp_repressor/repl_initiator.
    [Graphical view ]
    Pfami PF00308. Bac_DnaA. 1 hit.
    PF08299. Bac_DnaA_C. 1 hit.
    PF11638. DnaA_N. 1 hit.
    [Graphical view ]
    PRINTSi PR00051. DNAA.
    SMARTi SM00382. AAA. 1 hit.
    SM00760. Bac_DnaA_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48295. SSF48295. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsi TIGR00362. DnaA. 1 hit.
    PROSITEi PS01008. DNAA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of the dnaA gene and the first part of the dnaN gene of Escherichia coli K-12."
      Hansen E.B., Hansen F.G., von Meyenburg K.
      Nucleic Acids Res. 10:7373-7385(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Structural analysis of the dnaA and dnaN genes of Escherichia coli."
      Ohmori H., Kimura M., Nagata T., Sakakibara Y.
      Gene 28:159-170(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
      Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
      Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 403-407.
      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. "The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH gene, coding for the ribosomal protein L34, of Escherichia coli."
      Hansen F.G., Hansen E.B., Atlung T.
      EMBO J. 1:1043-1048(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
    7. "The E. coli dnaA initiation protein: a protein for all seasons."
      Georgopoulos C.
      Trends Genet. 5:319-321(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    8. "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.
    9. "Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2."
      Konieczny I., Doran K.S., Helinski D.R., Blasina A.
      J. Biol. Chem. 272:20173-20178(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN PLASMID DNA REPLICATION, DNA-BINDING.
    10. "Coordinated replication and sequestration of oriC and dnaA are required for maintaining controlled once-per-cell-cycle initiation in Escherichia coli."
      Riber L., Lobner-Olesen A.
      J. Bacteriol. 187:5605-5613(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN AUTO REGULATION OF TRANSCRIPTION.
      Strain: K12.
    11. "The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes."
      Keyamura K., Fujikawa N., Ishida T., Ozaki S., Su'etsugu M., Fujimitsu K., Kagawa W., Yokoyama S., Kurumizaka H., Katayama T.
      Genes Dev. 21:2083-2099(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH DIAA, FUNCTION.
    12. "Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis."
      Su'etsugu M., Nakamura K., Keyamura K., Kudo Y., Katayama T.
      J. Biol. Chem. 283:36118-36131(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN RIDA COMPLEX.
    13. "Structural basis of replication origin recognition by the DnaA protein."
      Fujikawa N., Kurumizaka H., Nureki O., Terada T., Shirouzu M., Katayama T., Yokoyama S.
      Nucleic Acids Res. 31:2077-2086(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 374-467.
    14. "Structure and function of dnaA N-terminal domains: specific sites and mechanisms in inter-DNAA interaction and in dnaB helicase loading on oric."
      RIKEN structural genomics initiative (RSGI)
      Submitted (MAY-2007) to the PDB data bank
      Cited for: STRUCTURE BY NMR OF 2-108.

    Entry informationi

    Entry nameiDNAA_ECOLI
    AccessioniPrimary (citable) accession number: P03004
    Secondary accession number(s): P78122, Q2M814
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 1, 1993
    Last modified: October 1, 2014
    This is version 144 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    At least 4 systems specifically target DnaA to prevent more than 1 round of replication initiation per cell cycle. 1: SeqA binds to and sequesters hemimethylated oriC, preventing DnaA binding. 2: ATP-DnaA binds to the chromosomal datA locus, sequestering ATP-DnaA. 3: ATP-DnaA binds to its own promoter, repressing transcription. 4: RIDA (regulatory inactivation of DnaA) via Hda and the DNA-loaded beta clamp hydrolyzes ATP-DnaA to ADP-DnaA.

    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