Summary: Bacterial dnaA protein helix-turn-helix
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|Chromosomal replication initiator protein dnaA|
(str. K-12 substr. MG1655)
|Chromosome||genome: 3.88 - 3.88 Mb|
|crystal structure of dnaa domainiv complexed with dnaabox dna|
|structure of amppcp-bound dnaa from aquifex aeolicus|
DnaA is a protein that activates initiation of DNA replication in prokaryotes. It is a replication initiation factor which promotes the unwinding of DNA at oriC. The onset of the initiation phase of DNA replication is determined by the concentration of DnaA. DnaA accumulates during growth and then triggers the initiation of replication. Replication begins with active DnaA binding to 9-mer (9-bp) repeats upstream of the oriC. Binding of DnaA leads to strand separation at the 13-mer repeats. This binding causes the DNA to loop in preparation for melting open by the helicase DnaB.
The oriC site in E. coli has three AT rich 13 base pair regions (DUEs) followed by four 9 bp regions.  Around 10 dnaA molecules bind to the 9 bp regions, which wrap around the proteins causing the DNA at the AT-rich region to unwind. There are 8 dnaA binding sites within oriC, to which dnaA binds with differential affinity. When DNA replication is about to commence, dnaA occupies all of the high and low affinity binding sites. The denatured AT-rich region allows for the recruitment of DnaB (helicase), which complexes with DnaC (helicase loader). DnaC helps the helicase to bind to and to properly accommodate the ssDNA at the 13 bp region; this is accomplished by ATP hydrolysis, after which DnaC is released. Single-strand binding proteins (SSBs) stabilize the single DNA strands in order to maintain the replication bubble. DnaB is a 5'→3' helicase, so it travels on the lagging strand. It associates with DnaG (a primase) to form the only primer for the leading strand and to add RNA primers on the lagging strand. The interaction between DnaG and DnaB is necessary to control the longitude of Okazaki fragments on the lagging strand. DNA polymerase III is then able to start DNA replication.
DnaA contains two conserved regions: the first is located in the central part of the protein and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding.
- Foster JB, Slonczewski J (2009). Microbiology: an evolving science. New York: W.W. Norton & Co. ISBN 0-393-97857-5.
- Fuller, RS; Funnell, BE; Kornberg, A (1984 Oct). "The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites.". Cell 38 (3): 889–900. PMID 6091903.
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Bacterial dnaA protein helix-turn-helix Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR013159
This entry represents the C-terminal domain of bacterial DnaA proteins [PUBMED:8110826, PUBMED:1779750, PUBMED:2558436] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC).
DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [PUBMED:2172087].
|Molecular function||ATP binding (GO:0005524)|
|sequence-specific DNA binding (GO:0043565)|
|Biological process||regulation of DNA replication (GO:0006275)|
|DNA-dependent DNA replication initiation (GO:0006270)|
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|Author:||Finn RD, Bateman A|
|Number in seed:||14|
|Number in full:||4828|
|Average length of the domain:||68.70 aa|
|Average identity of full alignment:||46 %|
|Average coverage of the sequence by the domain:||15.45 %|
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build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Bac_DnaA_C domain has been found. There are 14 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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