DNAA_ECOLI
ID DNAA_ECOLI Reviewed; 467 AA.
AC P03004; P78122; Q2M814;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1993, sequence version 2.
DT 03-AUG-2022, entry version 195.
DE RecName: Full=Chromosomal replication initiator protein DnaA;
GN Name=dnaA; OrderedLocusNames=b3702, JW3679;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=6296774; DOI=10.1093/nar/10.22.7373;
RA Hansen E.B., Hansen F.G., von Meyenburg K.;
RT "The nucleotide sequence of the dnaA gene and the first part of the dnaN
RT gene of Escherichia coli K-12.";
RL Nucleic Acids Res. 10:7373-7385(1982).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6234204; DOI=10.1016/0378-1119(84)90253-1;
RA Ohmori H., Kimura M., Nagata T., Sakakibara Y.;
RT "Structural analysis of the dnaA and dnaN genes of Escherichia coli.";
RL Gene 28:159-170(1984).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION TO
RP 403-407.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
RX PubMed=6329723; DOI=10.1002/j.1460-2075.1982.tb01294.x;
RA Hansen F.G., Hansen E.B., Atlung T.;
RT "The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH
RT gene, coding for the ribosomal protein L34, of Escherichia coli.";
RL EMBO J. 1:1043-1048(1982).
RN [7]
RP REVIEW.
RX PubMed=2558436; DOI=10.1016/0168-9525(89)90118-2;
RA Georgopoulos C.;
RT "The E. coli dnaA initiation protein: a protein for all seasons.";
RL Trends Genet. 5:319-321(1989).
RN [8]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [9]
RP FUNCTION IN PLASMID DNA REPLICATION, AND DNA-BINDING.
RX PubMed=9242693; DOI=10.1074/jbc.272.32.20173;
RA Konieczny I., Doran K.S., Helinski D.R., Blasina A.;
RT "Role of TrfA and DnaA proteins in origin opening during initiation of DNA
RT replication of the broad host range plasmid RK2.";
RL J. Biol. Chem. 272:20173-20178(1997).
RN [10]
RP FUNCTION IN AUTO REGULATION OF TRANSCRIPTION.
RC STRAIN=K12;
RX PubMed=16077105; DOI=10.1128/jb.187.16.5605-5613.2005;
RA Riber L., Lobner-Olesen A.;
RT "Coordinated replication and sequestration of oriC and dnaA are required
RT for maintaining controlled once-per-cell-cycle initiation in Escherichia
RT coli.";
RL J. Bacteriol. 187:5605-5613(2005).
RN [11]
RP INTERACTION WITH DIAA, AND FUNCTION.
RX PubMed=17699754; DOI=10.1101/gad.1561207;
RA Keyamura K., Fujikawa N., Ishida T., Ozaki S., Su'etsugu M., Fujimitsu K.,
RA Kagawa W., Yokoyama S., Kurumizaka H., Katayama T.;
RT "The interaction of DiaA and DnaA regulates the replication cycle in E.
RT coli by directly promoting ATP DnaA-specific initiation complexes.";
RL Genes Dev. 21:2083-2099(2007).
RN [12]
RP IDENTIFICATION IN RIDA COMPLEX.
RX PubMed=18977760; DOI=10.1074/jbc.m803158200;
RA Su'etsugu M., Nakamura K., Keyamura K., Kudo Y., Katayama T.;
RT "Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-
RT ATP hydrolysis.";
RL J. Biol. Chem. 283:36118-36131(2008).
RN [13]
RP ACETYLATION AT LYS-178, ACTIVITY REGULATION, AND MUTAGENESIS OF LYS-178.
RX PubMed=27484197; DOI=10.1038/srep30837;
RA Zhang Q., Zhou A., Li S., Ni J., Tao J., Lu J., Wan B., Li S., Zhang J.,
RA Zhao S., Zhao G.P., Shao F., Yao Y.F.;
RT "Reversible lysine acetylation is involved in DNA replication initiation by
RT regulating activities of initiator DnaA in Escherichia coli.";
RL Sci. Rep. 6:30837-30837(2016).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 374-467.
RX PubMed=12682358; DOI=10.1093/nar/gkg309;
RA Fujikawa N., Kurumizaka H., Nureki O., Terada T., Shirouzu M., Katayama T.,
RA Yokoyama S.;
RT "Structural basis of replication origin recognition by the DnaA protein.";
RL Nucleic Acids Res. 31:2077-2086(2003).
RN [15]
RP STRUCTURE BY NMR OF 2-108.
RG RIKEN structural genomics initiative (RSGI);
RT "Structure and function of dnaA N-terminal domains: specific sites and
RT mechanisms in inter-DNAA interaction and in dnaB helicase loading on
RT oric.";
RL Submitted (MAY-2007) to the PDB data bank.
CC -!- FUNCTION: Plays a key role in the initiation and regulation of
CC chromosomal replication. Binds in an ATP-dependent fashion to the
CC origin of replication (oriC) to initiate formation of the DNA
CC replication initiation complex exactly once per cell cycle. Binds the
CC DnaA box (consensus sequence 5'-TTATC[CA]A[CA]A-3'); subsequent binding
CC of DNA polymerase III subunits leads to replisome formation. The DnaA-
CC ATP form converts to DnaA-ADP; once converted to ADP the protein cannot
CC initiate replication, ensuring only 1 round of replication per cell
CC cycle. DnaA can inhibit its own gene expression as well as that of
CC other genes such as dam, rpoH, ftsA and mioC.
CC -!- FUNCTION: Also required for replication of plasmid DNA; binds 4 dnaA
CC boxes in the minimal plasmid RK2 replication origin (oriV).
CC -!- ACTIVITY REGULATION: Acetylation decreases the binding abilities to ATP
CC and ADP and leads to inhibition of DNA replication initiation.
CC {ECO:0000269|PubMed:27484197}.
CC -!- SUBUNIT: Some 20 DnaA protein molecules bind their sites in oriC. Forms
CC the RIDA (regulatory inactivation of DnaA) complex with ATP-DnaA, ADP-
CC Hda and the DNA-loaded sliding beta clamp (dnaN). Interacts with DiaA;
CC this stimulates the association of DnaA with the origin of replication.
CC {ECO:0000269|PubMed:17699754, ECO:0000269|PubMed:18977760}.
CC -!- INTERACTION:
CC P03004; P66817: diaA; NbExp=5; IntAct=EBI-548951, EBI-1125806;
CC P03004; P03004: dnaA; NbExp=2; IntAct=EBI-548951, EBI-548951;
CC P03004; P0ACB0: dnaB; NbExp=4; IntAct=EBI-548951, EBI-548978;
CC P03004; P0ABT2: dps; NbExp=2; IntAct=EBI-548951, EBI-549640;
CC P03004; P69931: hda; NbExp=2; IntAct=EBI-548951, EBI-545453;
CC P03004; P0ACF0: hupA; NbExp=5; IntAct=EBI-548951, EBI-547648;
CC P03004; P18843: nadE; NbExp=3; IntAct=EBI-548951, EBI-548960;
CC P03004; P60422: rplB; NbExp=5; IntAct=EBI-548951, EBI-543515;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- PTM: Acetylated at Lys-178 by PatZ. Deacetylated by CobB. Is also
CC acetylated nonenzymatically by acetyl-phosphate. Acetylation level
CC increases in a growth phase-dependent manner and peaks at the
CC stationnary phase. {ECO:0000269|PubMed:27484197}.
CC -!- MISCELLANEOUS: At least 4 systems specifically target DnaA to prevent
CC more than 1 round of replication initiation per cell cycle. 1: SeqA
CC binds to and sequesters hemimethylated oriC, preventing DnaA binding.
CC 2: ATP-DnaA binds to the chromosomal datA locus, sequestering ATP-DnaA.
CC 3: ATP-DnaA binds to its own promoter, repressing transcription. 4:
CC RIDA (regulatory inactivation of DnaA) via Hda and the DNA-loaded beta
CC clamp hydrolyzes ATP-DnaA to ADP-DnaA.
CC -!- SIMILARITY: Belongs to the DnaA family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA62053.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; J01602; AAB59149.1; -; Genomic_DNA.
DR EMBL; X01861; CAA25980.1; -; Genomic_DNA.
DR EMBL; L10328; AAA62053.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76725.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77592.1; -; Genomic_DNA.
DR PIR; G65172; IQECDA.
DR RefSeq; NP_418157.1; NC_000913.3.
DR RefSeq; WP_000059111.1; NZ_STEB01000015.1.
DR PDB; 1J1V; X-ray; 2.10 A; A=374-467.
DR PDB; 2E0G; NMR; -; A=2-108.
DR PDBsum; 1J1V; -.
DR PDBsum; 2E0G; -.
DR AlphaFoldDB; P03004; -.
DR SMR; P03004; -.
DR BioGRID; 4261539; 155.
DR BioGRID; 852519; 2.
DR ComplexPortal; CPX-1943; dnaA oligomeric complex.
DR ComplexPortal; CPX-1944; DnaA-L2 DNA replication initiation inhibitory complex.
DR ComplexPortal; CPX-1945; Regulatory inactivation of dnaA (RIDA) complex.
DR ComplexPortal; CPX-1948; dnaA-dps DNA replication initiation inhibitory complex.
DR ComplexPortal; CPX-1950; dnaA-dnaB-dnaC loader complex.
DR ComplexPortal; CPX-1961; DnaA-HU complex, variant hupAB.
DR ComplexPortal; CPX-1962; DnaA-HU complex, variant hupA.
DR ComplexPortal; CPX-1963; dnaA-diaA complex.
DR DIP; DIP-9455N; -.
DR IntAct; P03004; 45.
DR STRING; 511145.b3702; -.
DR iPTMnet; P03004; -.
DR jPOST; P03004; -.
DR PaxDb; P03004; -.
DR PRIDE; P03004; -.
DR DNASU; 948217; -.
DR EnsemblBacteria; AAC76725; AAC76725; b3702.
DR EnsemblBacteria; BAE77592; BAE77592; BAE77592.
DR GeneID; 66672400; -.
DR GeneID; 948217; -.
DR KEGG; ecj:JW3679; -.
DR KEGG; eco:b3702; -.
DR PATRIC; fig|511145.12.peg.3826; -.
DR EchoBASE; EB0231; -.
DR eggNOG; COG0593; Bacteria.
DR HOGENOM; CLU_026910_0_1_6; -.
DR InParanoid; P03004; -.
DR OMA; REFNPLF; -.
DR PhylomeDB; P03004; -.
DR BioCyc; EcoCyc:PD03831; -.
DR EvolutionaryTrace; P03004; -.
DR PRO; PR:P03004; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009898; C:cytoplasmic side of plasma membrane; IDA:EcoCyc.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:1990102; C:DnaA-DiaA complex; IPI:ComplexPortal.
DR GO; GO:1990084; C:DnaA-Dps complex; IPI:ComplexPortal.
DR GO; GO:1990103; C:DnaA-HU complex; IPI:ComplexPortal.
DR GO; GO:1990082; C:DnaA-L2 complex; IPI:ComplexPortal.
DR GO; GO:1990101; C:DnaA-oriC complex; IPI:ComplexPortal.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:1990078; C:replication inhibiting complex; IPI:ComplexPortal.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc.
DR GO; GO:0003688; F:DNA replication origin binding; IMP:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:EcoliWiki.
DR GO; GO:0006260; P:DNA replication; IMP:EcoliWiki.
DR GO; GO:0006270; P:DNA replication initiation; IDA:ComplexPortal.
DR GO; GO:0006268; P:DNA unwinding involved in DNA replication; IC:ComplexPortal.
DR GO; GO:0032297; P:negative regulation of DNA-templated DNA replication initiation; IDA:ComplexPortal.
DR GO; GO:0032298; P:positive regulation of DNA-templated DNA replication initiation; IDA:ComplexPortal.
DR GO; GO:0006275; P:regulation of DNA replication; IMP:EcoliWiki.
DR GO; GO:0030174; P:regulation of DNA-templated DNA replication initiation; IC:ComplexPortal.
DR CDD; cd06571; Bac_DnaA_C; 1.
DR Gene3D; 1.10.1750.10; -; 1.
DR Gene3D; 3.30.300.180; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00377; DnaA_bact; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR001957; Chromosome_initiator_DnaA.
DR InterPro; IPR020591; Chromosome_initiator_DnaA-like.
DR InterPro; IPR018312; Chromosome_initiator_DnaA_CS.
DR InterPro; IPR013317; DnaA.
DR InterPro; IPR013159; DnaA_C.
DR InterPro; IPR024633; DnaA_N_dom.
DR InterPro; IPR038454; DnaA_N_sf.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR010921; Trp_repressor/repl_initiator.
DR PANTHER; PTHR30050:SF2; PTHR30050:SF2; 1.
DR Pfam; PF00308; Bac_DnaA; 1.
DR Pfam; PF08299; Bac_DnaA_C; 1.
DR Pfam; PF11638; DnaA_N; 1.
DR PRINTS; PR00051; DNAA.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00760; Bac_DnaA_C; 1.
DR SUPFAM; SSF48295; SSF48295; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00362; DnaA; 1.
DR PROSITE; PS01008; DNAA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; ATP-binding; Cytoplasm; DNA replication;
KW DNA replication inhibitor; DNA-binding; Nucleotide-binding;
KW Reference proteome; Repressor; Transcription; Transcription regulation.
FT CHAIN 1..467
FT /note="Chromosomal replication initiator protein DnaA"
FT /id="PRO_0000114174"
FT REGION 98..119
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 98..114
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 172..179
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305"
FT MOD_RES 178
FT /note="N6-acetyllysine; by PatZ"
FT /evidence="ECO:0000269|PubMed:27484197"
FT MUTAGEN 178
FT /note="K->Q,R: Loses the ability to bind to ATP or ADP."
FT /evidence="ECO:0000269|PubMed:27484197"
FT CONFLICT 69..70
FT /note="AD -> RI (in Ref. 1)"
FT /evidence="ECO:0000305"
FT CONFLICT 403..407
FT /note="VARPR -> GXGPG (in Ref. 3; AAA62053)"
FT /evidence="ECO:0000305"
FT HELIX 5..16
FT /evidence="ECO:0007829|PDB:2E0G"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:2E0G"
FT TURN 25..28
FT /evidence="ECO:0007829|PDB:2E0G"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:2E0G"
FT STRAND 35..44
FT /evidence="ECO:0007829|PDB:2E0G"
FT HELIX 45..53
FT /evidence="ECO:0007829|PDB:2E0G"
FT HELIX 55..66
FT /evidence="ECO:0007829|PDB:2E0G"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:2E0G"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:2E0G"
FT HELIX 376..386
FT /evidence="ECO:0007829|PDB:1J1V"
FT HELIX 391..395
FT /evidence="ECO:0007829|PDB:1J1V"
FT HELIX 401..417
FT /evidence="ECO:0007829|PDB:1J1V"
FT HELIX 422..428
FT /evidence="ECO:0007829|PDB:1J1V"
FT HELIX 434..450
FT /evidence="ECO:0007829|PDB:1J1V"
FT HELIX 452..465
FT /evidence="ECO:0007829|PDB:1J1V"
SQ SEQUENCE 467 AA; 52551 MW; 607C8366A8CDCCED CRC64;
MSLSLWQQCL ARLQDELPAT EFSMWIRPLQ AELSDNTLAL YAPNRFVLDW VRDKYLNNIN
GLLTSFCGAD APQLRFEVGT KPVTQTPQAA VTSNVAAPAQ VAQTQPQRAA PSTRSGWDNV
PAPAEPTYRS NVNVKHTFDN FVEGKSNQLA RAAARQVADN PGGAYNPLFL YGGTGLGKTH
LLHAVGNGIM ARKPNAKVVY MHSERFVQDM VKALQNNAIE EFKRYYRSVD ALLIDDIQFF
ANKERSQEEF FHTFNALLEG NQQIILTSDR YPKEINGVED RLKSRFGWGL TVAIEPPELE
TRVAILMKKA DENDIRLPGE VAFFIAKRLR SNVRELEGAL NRVIANANFT GRAITIDFVR
EALRDLLALQ EKLVTIDNIQ KTVAEYYKIK VADLLSKRRS RSVARPRQMA MALAKELTNH
SLPEIGDAFG GRDHTTVLHA CRKIEQLREE SHDIKEDFSN LIRTLSS
