P03004 (DNAA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Chromosomal replication initiator protein DnaA

Gene names

Name:	dnaA
Ordered Locus Names:	b3702, JW3679

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	467 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. DnaA can inhibit its own gene expression as well as that of other genes such as dam, rpoH, ftsA and mioC. HAMAP MF_00377
Subunit structure	Some 20 DnaA protein molecules bind their sites in oriC. Forms a large complex with ATP-DnaA, ADP-Hda and the DNA-loaded clamp.
Subcellular location	Cytoplasm HAMAP MF_00377.
Sequence similarities	Belongs to the DnaA family.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Nucleotide-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA-dependent DNA replication initiation Inferred from electronic annotation. Source: InterPro regulation of DNA replication Inferred from mutant phenotype. Source: EcoliWiki
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA replication origin binding Inferred from electronic annotation. Source: InterPro nucleoside-triphosphatase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 467

467

Chromosomal replication initiator protein DnaA HAMAP MF_00377

PRO_0000114174

Regions

Nucleotide binding

172 – 179

8

ATP Probable

Experimental info

Sequence conflict

69 – 70

2

AD → RI Ref.1

Secondary structure

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467

Helix Strand Turn

Details...

Helix

5 – 16

12

Helix

21 – 24

4

Turn

25 – 28

4

Beta strand

29 – 33

5

Beta strand

35 – 44

10

Helix

45 – 53

9

Helix

55 – 66

12

Beta strand

68 – 70

3

Beta strand

77 – 80

4

Helix

376 – 386

11

Helix

391 – 395

5

Helix

401 – 417

17

Helix

422 – 428

7

Helix

434 – 450

17

Helix

452 – 465

14

Sequences

	Sequence		Length	Mass (Da)
	P03004 [UniParc]. Last modified July 1, 1993. Version 2. Checksum: 607C8366A8CDCCED	FASTA	467	52,551
	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

References

	« Hide 'large scale' referencesShow '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: 6296774] [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: 6234204] [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: 7686882] [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 277:1453-1474(1997) [PubMed: 9278503] [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: 16738553] [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: 6329723] [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: 2558436] [Abstract] Cited for: REVIEW.
[8]	"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: 18977760] [Abstract] Cited for: IDENTIFICATION IN A CLAMP-COMPLEX.
[9]	"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: 12682358] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 374-467.
[10]	"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. Sequence problems.
U00096 Genomic DNA. Translation: AAC76725.1.
AP009048 Genomic DNA. Translation: BAE77592.1.

PIR

IQECDA. G65172.

RefSeq

NP_418157.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J1V	X-ray	2.10	A	374-467	[»]
2E0G	NMR	-	A	2-108	[»]

ProteinModelPortal

P03004.

SMR

P03004. Positions 2-108, 130-467.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9455N.

IntAct

P03004. 34 interactions.

MINT

MINT-207293.

2D gel databases

ECO2DBASE

I049.0. 6TH EDITION.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000004202; EBESCP00000004202; EBESCG00000003429.
EBESCT00000004203; EBESCP00000004203; EBESCG00000003429.
EBESCT00000014399; EBESCP00000013690; EBESCG00000013460.

GeneID

948217.

GenomeReviews

Gene locus JW3679 in contig AP009048_GR.
Gene locus b3702 in contig U00096_GR.

KEGG

ecj:JW3679.
eco:b3702.

PATRIC

32122901. VBIEscCol129921_3826.

Organism-specific databases

EchoBASE

EB0231.

EcoGene

EG10235. dnaA.

Phylogenomic databases

eggNOG

COG0593.

GeneTree

EBGT00050000009281.

HOGENOM

HBG695666.

OMA

CHTLNAL.

PhylomeDB

P03004.

ProtClustDB

PRK00149.

Enzyme and pathway databases

BioCyc

EcoCyc:PD03831.

Gene expression databases

Genevestigator

P03004.

Family and domain databases

HAMAP

MF_00377. DnaA_bact.
[Tree]

InterPro

IPR003593. ATPase_AAA+_core.
IPR001957. Chromosome_initiator_DnaA.
IPR020591. Chromosome_initiator_DnaA-like.
IPR018312. Chromosome_initiator_DnaA_CS.
IPR013159. DnaA_C.
IPR013317. DnaA_Hda.
IPR010921. Trp_repressor/repl_initiator.
[Graphical view]

Gene3D

G3DSA:1.10.1750.10. DnaA_C. 1 hit.

KO

K02313.

Pfam

PF00308. Bac_DnaA. 1 hit.
PF08299. Bac_DnaA_C. 1 hit.
[Graphical view]

PRINTS

PR00051. DNAA.

SMART

SM00382. AAA. 1 hit.
SM00760. Bac_DnaA_C. 1 hit.
[Graphical view]

SUPFAM

SSF48295. Trp_repress_rep. 1 hit.

TIGRFAMs

TIGR00362. DnaA. 1 hit.

PROSITE

PS01008. DNAA. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DNAA_ECOLI

Accession

Primary (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:	January 25, 2012
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program