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P03004 (DNAA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Chromosomal replication initiator protein DnaA
Gene names
Name:dnaA
Ordered Locus Names:b3702, JW3679
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length467 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.9 Ref.10 Ref.11

Also required for replication of plasmid DNA; binds 4 dnaA boxes in the minimal plasmid RK2 replication origin (oriV). Ref.9 Ref.10 Ref.11

Subunit structure

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. Ref.11 Ref.12

Subcellular location

Cytoplasm HAMAP-Rule MF_00377.

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.

Sequence similarities

Belongs to the DnaA family.

Sequence caution

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

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 467467Chromosomal replication initiator protein DnaA HAMAP-Rule MF_00377
PRO_0000114174

Regions

Nucleotide binding172 – 1798ATP Probable

Experimental info

Sequence conflict69 – 702AD → RI Ref.1
Sequence conflict403 – 4075VARPR → GXGPG in AAA62053. Ref.3

Secondary structure

............................ 467
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P03004 [UniParc].

Last modified July 1, 1993. Version 2.
Checksum: 607C8366A8CDCCED

FASTA46752,551
        10         20         30         40         50         60 
MSLSLWQQCL ARLQDELPAT EFSMWIRPLQ AELSDNTLAL YAPNRFVLDW VRDKYLNNIN 

        70         80         90        100        110        120 
GLLTSFCGAD APQLRFEVGT KPVTQTPQAA VTSNVAAPAQ VAQTQPQRAA PSTRSGWDNV 

       130        140        150        160        170        180 
PAPAEPTYRS NVNVKHTFDN FVEGKSNQLA RAAARQVADN PGGAYNPLFL YGGTGLGKTH 

       190        200        210        220        230        240 
LLHAVGNGIM ARKPNAKVVY MHSERFVQDM VKALQNNAIE EFKRYYRSVD ALLIDDIQFF 

       250        260        270        280        290        300 
ANKERSQEEF FHTFNALLEG NQQIILTSDR YPKEINGVED RLKSRFGWGL TVAIEPPELE 

       310        320        330        340        350        360 
TRVAILMKKA DENDIRLPGE VAFFIAKRLR SNVRELEGAL NRVIANANFT GRAITIDFVR 

       370        380        390        400        410        420 
EALRDLLALQ EKLVTIDNIQ KTVAEYYKIK VADLLSKRRS RSVARPRQMA MALAKELTNH 

       430        440        450        460 
SLPEIGDAFG GRDHTTVLHA CRKIEQLREE SHDIKEDFSN LIRTLSS 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRIQECDA. G65172.
RefSeqNP_418157.1. NC_000913.3.
YP_491733.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1J1VX-ray2.10A374-467[»]
2E0GNMR-A2-108[»]
ProteinModelPortalP03004.
SMRP03004. Positions 2-108, 132-467.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9455N.
IntActP03004. 44 interactions.
MINTMINT-207293.
STRING511145.b3702.

Proteomic databases

PaxDbP03004.
PRIDEP03004.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76725; AAC76725; b3702.
BAE77592; BAE77592; BAE77592.
GeneID12932545.
948217.
KEGGecj:Y75_p3471.
eco:b3702.
PATRIC32122901. VBIEscCol129921_3826.

Organism-specific databases

EchoBASEEB0231.
EcoGeneEG10235. dnaA.

Phylogenomic databases

eggNOGCOG0593.
HOGENOMHOG000235659.
KOK02313.
OMASWFARMD.
OrthoDBEOG689HR1.
PhylomeDBP03004.
ProtClustDBPRK00149.

Enzyme and pathway databases

BioCycEcoCyc:PD03831.
ECOL316407:JW3679-MONOMER.

Gene expression databases

GenevestigatorP03004.

Family and domain databases

Gene3D1.10.1750.10. 1 hit.
3.40.50.300. 1 hit.
HAMAPMF_00377. DnaA_bact.
InterProIPR003593. 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]
PfamPF00308. Bac_DnaA. 1 hit.
PF08299. Bac_DnaA_C. 1 hit.
PF11638. DnaA_N. 1 hit.
[Graphical view]
PRINTSPR00051. DNAA.
SMARTSM00382. AAA. 1 hit.
SM00760. Bac_DnaA_C. 1 hit.
[Graphical view]
SUPFAMSSF48295. SSF48295. 1 hit.
SSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00362. DnaA. 1 hit.
PROSITEPS01008. DNAA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP03004.
PROP03004.

Entry information

Entry nameDNAA_ECOLI
AccessionPrimary (citable) accession number: P03004
Secondary accession number(s): P78122, Q2M814
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 1, 1993
Last modified: April 16, 2014
This is version 141 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene