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P03004

- DNAA_ECOLI

UniProt

P03004 - DNAA_ECOLI

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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

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. 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
Complete GO annotation...

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-HAMAP
  2. plasma membrane Source: EcoCyc
Complete GO annotation...

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.
SMRiP03004. Positions 2-108, 132-467.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03004.

Family & Domainsi

Sequence similaritiesi

Belongs to the DnaA family.Curated

Phylogenomic databases

eggNOGiCOG0593.
HOGENOMiHOG000235659.
InParanoidiP03004.
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

        10         20         30         40         50
MSLSLWQQCL ARLQDELPAT EFSMWIRPLQ AELSDNTLAL YAPNRFVLDW
60 70 80 90 100
VRDKYLNNIN GLLTSFCGAD APQLRFEVGT KPVTQTPQAA VTSNVAAPAQ
110 120 130 140 150
VAQTQPQRAA PSTRSGWDNV PAPAEPTYRS NVNVKHTFDN FVEGKSNQLA
160 170 180 190 200
RAAARQVADN PGGAYNPLFL YGGTGLGKTH LLHAVGNGIM ARKPNAKVVY
210 220 230 240 250
MHSERFVQDM VKALQNNAIE EFKRYYRSVD ALLIDDIQFF ANKERSQEEF
260 270 280 290 300
FHTFNALLEG NQQIILTSDR YPKEINGVED RLKSRFGWGL TVAIEPPELE
310 320 330 340 350
TRVAILMKKA DENDIRLPGE VAFFIAKRLR SNVRELEGAL NRVIANANFT
360 370 380 390 400
GRAITIDFVR EALRDLLALQ EKLVTIDNIQ KTVAEYYKIK VADLLSKRRS
410 420 430 440 450
RSVARPRQMA MALAKELTNH SLPEIGDAFG GRDHTTVLHA CRKIEQLREE
460
SHDIKEDFSN LIRTLSS
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.
SMRi P03004. Positions 2-108, 132-467.
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.
InParanoidi P03004.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 145 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