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14  structures 4481  species 1  interaction 4828  sequences 14  architectures

Family: Bac_DnaA_C (PF08299)

Summary: Bacterial dnaA protein helix-turn-helix

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This is the Wikipedia entry entitled "DnaA". More...

DnaA Edit Wikipedia article

Chromosomal replication initiator protein dnaA
Identifiers
Organism Escherichia coli
(str. K-12 substr. MG1655)
Symbol DnaA
Entrez 948217
RefSeq (Prot) NP_418157.1
UniProt P03004
Other data
Chromosome genome: 3.88 - 3.88 Mb
Bac_DnaA_C
PDB 1j1v EBI.jpg
crystal structure of dnaa domainiv complexed with dnaabox dna
Identifiers
Symbol Bac_DnaA_C
Pfam PF08299
Pfam clan CL0123
InterPro IPR013159
SCOP 1j1v
SUPERFAMILY 1j1v
Bac_DnaA
PDB 2hcb EBI.jpg
structure of amppcp-bound dnaa from aquifex aeolicus
Identifiers
Symbol Bac_DnaA
Pfam PF00308
Pfam clan CL0023
InterPro IPR013317
PROSITE PDOC00771
SCOP 1j1v
SUPERFAMILY 1j1v

DnaA is a protein that activates initiation of DNA replication in prokaryotes.[1] It is a replication initiation factor which promotes the unwinding of DNA at oriC.[1] The onset of the initiation phase of DNA replication is determined by the concentration of DnaA.[1] DnaA accumulates during growth and then triggers the initiation of replication.[1] Replication begins with active DnaA binding to 9-mer (9-bp) repeats upstream of oriC.[1] Binding of DnaA leads to strand separation at the 13-mer repeats.[1] This binding causes the DNA to loop in preparation for melting open by the helicase DnaB.[1]

Function

The active form DnaA is bound to ATP.[1] Immediately after a cell has divided, the level of active DnaA within the cell is low.[1] Although the active form of DnaA requires ATP, the formation of the oriC/DnaA complex and subsequent DNA unwinding does not require ATP hydrolysis.[2]

The oriC site in E. coli has three AT rich 13 base pair regions (DUEs) followed by four 9 bp regions.[3] 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 is involved in DNA-binding.[4]

References

  1. ^ a b c d e f g h i Foster JB, Slonczewski J (2009). Microbiology: an evolving science. New York: W.W. Norton & Co. ISBN 0-393-97857-5. 
  2. ^ Leonard AC, Grimwade JE (December 2010). "Regulating DnaA complex assembly: it is time to fill the gaps". Curr. Opin. Microbiol. 13 (6): 766–72. doi:10.1016/j.mib.2010.10.001. PMC 3005629. PMID 21035377. 
  3. ^ Fuller RS, Funnell BE, Kornberg A (October 1984). "The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites". Cell 38 (3): 889–900. doi:10.1016/0092-8674(84)90284-8. PMID 6091903. 
  4. ^ Roth A, Messer W (May 1995). "The DNA binding domain of the initiator protein DnaA". EMBO J. 14 (9): 2106–11. PMC 398312. PMID 7744016. 

Further reading

  • Pratt CA, Voet D, Voet JG (2012). Fundamentals of Biochemistry: Life at the Molecular Level. New York: Wiley. ISBN 0-470-54784-7. 
  • Cox M, Nelson DR (2008). Lehninger Principles of Biochemistry. W H Freeman & Co (Sd). ISBN 1-4292-2416-9. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR013159

This article incorporates text from the public domain Pfam and InterPro IPR013317

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Bacterial dnaA protein helix-turn-helix Provide feedback

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External database links

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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Pfam Clan

This family is a member of clan HTH (CL0123), which has the following description:

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

The clan contains the following 202 members:

AphA_like Arg_repressor B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD CENP-B_N Cro Crp DDRGK Dimerisation DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF3116 DUF3853 DUF387 DUF3908 DUF4095 DUF4364 DUF739 DUF742 DUF977 E2F_TDP ELK Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC Ftsk_gamma FUR GcrA GerE GntR HARE-HTH HemN_C Homeobox Homeobox_KN Homez HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_OrfB_IS605 HTH_psq HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IF2_N KorB LacI LexA_DNA_bind LZ_Tnp_IS481 MADF_DNA_bdg MarR MarR_2 Med9 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 Mor MotA_activ MRP-L20 Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-binding Neugrin NUMOD1 OST-HTH P22_Cro PaaX PadR PAX PCI PCI_Csn8 Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP SAC3_GANP SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SpoIIID Sulfolobus_pRN TBPIP Terminase_5 TetR_N TFIIE_alpha Tn916-Xis Trans_reg_C TrfA TrmB Trp_repressor UPF0122 z-alpha

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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Full
(4828)
Representative proteomes NCBI
(3266)
Meta
(2314)
RP15
(367)
RP35
(704)
RP55
(891)
RP75
(1038)
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  Seed
(14)
Full
(4828)
Representative proteomes NCBI
(3266)
Meta
(2314)
RP15
(367)
RP35
(704)
RP55
(891)
RP75
(1038)
Alignment:
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  Seed
(14)
Full
(4828)
Representative proteomes NCBI
(3266)
Meta
(2314)
RP15
(367)
RP35
(704)
RP55
(891)
RP75
(1038)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Domain
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 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.9 20.6
Noise cut-off 20.4 20.4
Model length: 70
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Bac_DnaA

Structures

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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