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Protein

Chromosomal replication initiator protein DnaA

Gene

dnaA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Nucleotide bindingi172 – 179ATPCurated8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • DNA binding Source: EcoCyc
  • DNA replication origin binding Source: EcoCyc
  • sequence-specific DNA binding Source: EcoliWiki

GO - Biological processi

  • DNA replication Source: EcoliWiki
  • DNA replication initiation Source: GO_Central
  • negative regulation of DNA replication Source: UniProtKB-KW
  • regulation of DNA replication Source: EcoliWiki
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10235. dnaA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001141741 – 467Chromosomal replication initiator protein DnaAAdd BLAST467

Proteomic databases

PaxDbiP03004.
PRIDEiP03004.

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

BioGridi4261539. 146 interactors.
DIPiDIP-9455N.
IntActiP03004. 44 interactors.
MINTiMINT-207293.
STRINGi511145.b3702.

Structurei

Secondary structure

1467
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 16Combined sources12
Helixi21 – 24Combined sources4
Turni25 – 28Combined sources4
Beta strandi29 – 33Combined sources5
Beta strandi35 – 44Combined sources10
Helixi45 – 53Combined sources9
Helixi55 – 66Combined sources12
Beta strandi68 – 70Combined sources3
Beta strandi77 – 80Combined sources4
Helixi376 – 386Combined sources11
Helixi391 – 395Combined sources5
Helixi401 – 417Combined sources17
Helixi422 – 428Combined sources7
Helixi434 – 450Combined sources17
Helixi452 – 465Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1J1VX-ray2.10A374-467[»]
2E0GNMR-A2-108[»]
ProteinModelPortaliP03004.
SMRiP03004.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03004.

Family & Domainsi

Sequence similaritiesi

Belongs to the DnaA family.Curated

Phylogenomic databases

eggNOGiENOG4105CI4. Bacteria.
COG0593. LUCA.
HOGENOMiHOG000235659.
InParanoidiP03004.
KOiK02313.
OMAiQSKTRKR.
PhylomeDBiP03004.

Family and domain databases

CDDicd06571. Bac_DnaA_C. 1 hit.
Gene3Di1.10.1750.10. 1 hit.
3.40.50.300. 1 hit.
HAMAPiMF_00377. DnaA_bact. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR001957. Chromosome_initiator_DnaA.
IPR020591. Chromosome_initiator_DnaA-like.
IPR018312. Chromosome_initiator_DnaA_CS.
IPR013317. DnaA.
IPR013159. DnaA_C.
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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti69 – 70AD → RI (PubMed:6296774).Curated2
Sequence conflicti403 – 407VARPR → GXGPG in AAA62053 (PubMed:7686882).Curated5

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000059111.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76725; AAC76725; b3702.
BAE77592; BAE77592; BAE77592.
GeneIDi948217.
KEGGiecj:JW3679.
eco:b3702.
PATRICi32122901. VBIEscCol129921_3826.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000059111.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1J1VX-ray2.10A374-467[»]
2E0GNMR-A2-108[»]
ProteinModelPortaliP03004.
SMRiP03004.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261539. 146 interactors.
DIPiDIP-9455N.
IntActiP03004. 44 interactors.
MINTiMINT-207293.
STRINGi511145.b3702.

Proteomic databases

PaxDbiP03004.
PRIDEiP03004.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76725; AAC76725; b3702.
BAE77592; BAE77592; BAE77592.
GeneIDi948217.
KEGGiecj:JW3679.
eco:b3702.
PATRICi32122901. VBIEscCol129921_3826.

Organism-specific databases

EchoBASEiEB0231.
EcoGeneiEG10235. dnaA.

Phylogenomic databases

eggNOGiENOG4105CI4. Bacteria.
COG0593. LUCA.
HOGENOMiHOG000235659.
InParanoidiP03004.
KOiK02313.
OMAiQSKTRKR.
PhylomeDBiP03004.

Enzyme and pathway databases

BioCyciEcoCyc:PD03831.
ECOL316407:JW3679-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP03004.
PROiP03004.

Family and domain databases

CDDicd06571. Bac_DnaA_C. 1 hit.
Gene3Di1.10.1750.10. 1 hit.
3.40.50.300. 1 hit.
HAMAPiMF_00377. DnaA_bact. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR001957. Chromosome_initiator_DnaA.
IPR020591. Chromosome_initiator_DnaA-like.
IPR018312. Chromosome_initiator_DnaA_CS.
IPR013317. DnaA.
IPR013159. DnaA_C.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 161 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.