|Gene:||dnaB||Accession Numbers: EG10236 (EcoCyc), b4052, ECK4044|
Synonyms: groP, grpA, grpD
Component of: primosome (summary available)
Subunit composition of replicative DNA helicase = [DnaB]6
DnaB, the replicative DNA helicase, processively unwinds DNA at replication forks in advance of DNA polymerase. Along with primase, it is responsible for the initation of chromosomal DNA replication and for the continued priming of lagging-strand synthesis [Fujimura79]. It is also required for DNA replication in a number of plasmids [Conrad79, Hasunuma79, Pritchard80].
DnaB is a component of the primosome, the protein complex that initiates replicative DNA synthesis at the origin of replication, oriC. Such initiation requires DnaA, DNA gyrase, DnaB and DnaC [Kaguni85]. Four or five DnaA monomers bind to a single DnaB helicase as well as binding to oriC, loading the DnaB onto one of the DNA strands exposed at the prepared origin of replication [Sutton98, Carr01, Carr02]. The resulting complex of DnaA, DnaB and DnaC binds asymmetrically along the DNA, extending fifty base pairs farther "upstream" from oriC [Funnell87]. Formation of this initiation complex on an oriC plasmid requires supercoiled DNA [Funnell86]. DnaB subsequently unwinds DNA bidirectionally from oriC. DNA gyrase is required for this bidirectional activity. In the absence of DNA synthesis, single-strand binding protein (SSB) binds the unwound DNA [Baker87]. DnaB remains continuously associated with the advancing replication forks during subsequent DNA synthesis [Wu92].
DnaC acts as a loader for DnaB, binding to it and localizing it to duplex DNA for its role in initiating replication and to single-stranded DNA for its role in assisting primer formation by primase [Wickner75, Marszalek94, Wahle89, Wahle89a]. Though it is required for loading DnaB onto DNA, bound DnaC directly limits DnaB's ATPase activity [Biswas87, Biswas86]. As a consequence, replication speed is depends on the DnaB:DnaC ratio in vivo [Allen91, Skarstad95]. Six DnaC bind to one helicase hexamer, binding as a trio of dimers. While DnaC is bound, the opposite entrance to the helicase channel is nearly completely blocked, preventing efficient passage of DNA [Barcena01, San98]. ATP hydrolysis is not required for release of DnaC [Galletto03].
The role of DnaB in initiation of phage λ DNA replication has also been extensively characterized. The formation of the lambda primosome analog, the "O-some," begins with binding of several O proteins at ori lambda. DnaB and lambda P, a DnaC analog, subsequently bind the O proteins [Dodson85, Mallory90]. The members of the DnaK chaperone system (DnaJ, DnaK, GrpE) then bind, with GrpE being required for bidirectional unwinding by DnaB [Dodson86, Wyman93, Liberek90, Alfano89].
DnaB can also be reloaded onto arrested replication forks. PriA opens a collapsed replication fork to allow subsequent DnaB binding [Jones99]. Though PriA restarting requires PriB and DnaT as well as a gapless leading strand, PriC can reload DnaB by itself [Heller05].
DnaB interacts with DNA primase (DnaG) [Lu96]. As DnaB processively unwinds DNA, primase follows, putting down primers on the lagging strand [McMacken77]. DnaB relaxes the specificity of primase from GTC to PuPyPy [Yoda91]. DnaB also stimulates RNA primer synthesis by primase over 5,000 fold [Johnson00]. Indeed, the DnaB-DnaG interaction is the sole determinant in the rate of Okazaki fragment priming [Tougu96]. Three DnaG monomers interact with each DnaB helicase [Mitkova03]. Accurate initiation of bidirectional DNA replication from oriC requires proper primer placement for leading strand synthesis and thus depends on the helicase-primase interaction [Hiasa99]. The DnaB-DnaG interaction may also explain the need for DnaB in postreplication gap repair [Johnson75].
DnaB moves processively in the 5' to 3' direction on ssDNA. Its helicase activity is stimulated by SSB, but can be inhibited by prior binding of SSB to single-stranded regions of substrate DNA [LeBowitz86, Arai81]. This inhibition by SSB helps limit futile ATPase activity when DnaB is unable to progress, thus coupling its helicase and ATPase activities [Biswas02]. Helicase binding to ssDNA requires ATP binding but not ATP hydrolysis and involves a binding-induced conformational change in DnaB [Arai81a, Jezewska97, Galletto04]. The rate of DnaB helicase activity depends on the length of available 3' ssDNA in the replication fork. At least five nucleotides must be accessible for the maximal rate, though processivity has been demonstrated to depend on fourteen or more available nucleotides [Biswas02, Galletto04a]. DnaB's rate is inversely proportional to the stability of the duplex it is unwinding [Galletto04a]. In addition, mutations that disrupt helical phasing or DNA curvature slow DnaB helicase activity dramatically [Doran98]. The ssDNA strand on which DnaB travels passes through the inside of the hexameric helicase ring structure [Jezewska98]. The kinetics of DNA binding and nucleotide binding and hydrolysis have been examined in detail [Rajendran00, Bujalowski00, Bujalowski00a].
DnaB helicase comprises a hexamer of DnaB monomers, as confirmed by sedimentation analysis and crystallization [Ueda78, RehaKrantz78, Arai81b]. Existence as a hexamer depends on magnesium ion; in its absence, DnaB arranges into trimers [Bujalowski94]. The DnaB hexamer can have three-fold or six-fold symmetry depending on buffer conditions [Yu96]. This change is independent of ATP binding, though the helicase does undergo a conformational change when it binds ATP that leads to a four-fold increase in its affinity for single-stranded DNA [Donate00, Jezewska96]. DnaB only binds DNA as the full hexamer, binding in a specific orientation with the larger DnaB subdomain toward the 3' end of the bound strand [Jezewska96a, Jezewska98a]. The DNA-binding domain of DnaB consists of two subsites binding ten nucleotides each, one stronger and one weaker, both located on the inside of the hexamer ring. In the normal orientation, duplex DNA encounters the weaker site first [Jezewska98b, Kaplan04]. This nucleotide-binding site has been evaluated in detail [Bujalowski94a]. At any given moment, the helicase hexamer interacts with DNA at only one of its subunits [Bujalowski95].
Each DnaB monomer has key amino-terminal and carboxy-terminal domains. The carboxy-terminal domain contains a critical leucine zipper and is required for DNA binding, ATP binding and oligomerization [Nakayama84, Biswas99, Biswas99a]. The amino-terminus is required for hexamer formation and experiences significant conformational change during nucleotide binding and hydrolysis [Biswas94, Flowers03]. The structure of the amino-terminus has been examined via crystallography, electron microscopy and NMR [Miles97, Weigelt98, Fass99, Yang02]. DnaB monomers with mutations in the linker region still form hexamers but lose the ability to stimulate primase [Stordal96].
Certain proteins block the progress of DnaB along DNA. Bound Lac repressor inhibits unwinding through its binding region [YanceyWrona92]. Tus binds to the replication termination sequence ter and prevents helicase and the replication fork from proceeding [Lee89, Hiasa92, Skokotas94]. Tus blocking of DnaB depends on a specific interaction between the two proteins, rather than simple steric hindrance [Mulugu01]. A second protein can bind the ter site and allow DnaB to pass through it [Natarajan93]. Blocked DnaB function, or any stall in replication, leads to increased double-strand breaks, deletes in repeat sequences and recombination [Saveson97, Michel97, Lovett02].
DnaB can encircle both strands of duplex DNA in vitro. When it is bound in this manner, it can displace DNA-binding proteins and induce the movement of a synthetic Holliday junction [Kaplan02]. Helicase can even surround three DNA strands, allowing it to convert an invading strand during homologous recombination into a daughter lagging strand [Kaplan04]. Indeed, overexpression of DnaB increases the frequency of homologous recombination [Yamashita99].
Non-synonymous point mutations in dnaB were identified in cell populations that were selected for high resistance to ionizing radiation. The P80H allele was tested and was found to contribute significantly to resistance [Byrne14a].
|Map Position: [4,262,337 -> 4,263,752] (91.87 centisomes, 331°)||Length: 1416 bp / 471 aa|
Molecular Weight of Polypeptide: 52.39 kD (from nucleotide sequence)
pI: 4.9 [RehaKrantz78]
Unification Links: ASAP:ABE-0013269 , CGSC:850 , DIP:DIP-35913N , EchoBASE:EB0232 , EcoGene:EG10236 , EcoliWiki:b4052 , Mint:MINT-584605 , ModBase:P0ACB0 , OU-Microarray:b4052 , PortEco:dnaB , PR:PRO_000022460 , Pride:P0ACB0 , Protein Model Portal:P0ACB0 , RefSeq:NP_418476 , RegulonDB:EG10236 , SMR:P0ACB0 , String:511145.b4052 , Swiss-Model:P0ACB0 , UniProt:P0ACB0
Relationship Links: InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR007692 , InterPro:IN-FAMILY:IPR007693 , InterPro:IN-FAMILY:IPR007694 , InterPro:IN-FAMILY:IPR016136 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:1B79 , PDB:Structure:1JWE , Pfam:IN-FAMILY:PF00772 , Pfam:IN-FAMILY:PF03796 , Prosite:IN-FAMILY:PS51199 , Smart:IN-FAMILY:SM00382
|Biological Process:||GO:0006260 - DNA replication
[UniProtGOA11a, GOA01a, Hasunuma79]
GO:0006268 - DNA unwinding involved in DNA replication [LeBowitz86]
GO:0010212 - response to ionizing radiation [Byrne14a]
GO:0006269 - DNA replication, synthesis of RNA primer [UniProtGOA11a]
|Molecular Function:||GO:0003678 - DNA helicase activity
GO:0004386 - helicase activity [UniProtGOA11a, LeBowitz86]
GO:0005515 - protein binding [Rajagopala14, AriasPalomo13, Ng96, MakowskaGrzyska10, Guy09, Butland05, Mitkova03, Gao01, Seitz00]
GO:0042802 - identical protein binding [Bujalowski94, Mitkova03]
GO:0000166 - nucleotide binding [UniProtGOA11a]
GO:0003677 - DNA binding [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol
GO:1990077 - primosome complex [UniProtGOA11a]
|MultiFun Terms:||information transfer → DNA related → DNA replication|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Enzymatic reaction of: helicase
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
Reversibility of this reaction is unspecified.
Subunit of: primosome
Subunit composition of
primosome = [(DnaB)6][(DnaT)3][(PriB)2][PriA][PriC][DnaG]
replicative DNA helicase = (DnaB)6 (extended summary available)
primosomal protein DnaT = (DnaT)3 (extended summary available)
primosomal protein DnaT = DnaT
primosomal replication protein N = (PriB)2 (extended summary available)
primosome factor N' = PriA (extended summary available)
primosomal replication protein N'' = PriC (extended summary available)
DNA primase = DnaG (extended summary available)
The primosome is a six-protein complex that appears to be involved in restart of stalled replication forks, as well as in replication initiation in certain phages and plasmids. See the individual subunit entries for additional information on the function of the primosome.
The primosome undergoes ordered assembly beginning with PriA binding to DNA. Following this, PriB binds to PriA, then DnaT binds. After this, DnaC loads DnaB in an ATP-dependent manner. DnaG associates with the complex and synthesizes an RNA primer [Ng96a]. Despite its absence from this model of ordered assembly, PriC is also found in isolated intact primosomes [Ng96]. Note that the primosome components have many functions in the cell that do not require the full primosome.
|Conserved-Region||200 -> 467|
|Nucleotide-Phosphate-Binding-Region||231 -> 238|
|DNA-Binding-Region||324 -> 329|
10/20/97 Gene b4052 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10236; confirmed by SwissProt match.
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Ng96: Ng JY, Marians KJ (1996). "The ordered assembly of the phiX174-type primosome. II. Preservation of primosome composition from assembly through replication." J Biol Chem 271(26);15649-55. PMID: 8663105
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San98: San Martin C, Radermacher M, Wolpensinger B, Engel A, Miles CS, Dixon NE, Carazo JM (1998). "Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC." Structure 6(4);501-9. PMID: 9562559
Skokotas94: Skokotas A, Wrobleski M, Hill TM (1994). "Isolation and characterization of mutants of Tus, the replication arrest protein of Escherichia coli." J Biol Chem 269(32);20446-55. PMID: 8051142
Sutton98: Sutton MD, Carr KM, Vicente M, Kaguni JM (1998). "Escherichia coli DnaA protein. The N-terminal domain and loading of DnaB helicase at the E. coli chromosomal origin." J Biol Chem 273(51);34255-62. PMID: 9852089
Wahle89: Wahle E, Lasken RS, Kornberg A (1989). "The dnaB-dnaC replication protein complex of Escherichia coli. II. Role of the complex in mobilizing dnaB functions." J Biol Chem 264(5);2469-75. PMID: 2536713
Weigelt98: Weigelt J, Miles CS, Dixon NE, Otting G (1998). "Backbone NMR assignments and secondary structure of the N-terminal domain of DnaB helicase from E. coli." J Biomol NMR 11(2);233-4. PMID: 9679300
Wu92: Wu CA, Zechner EL, Marians KJ (1992). "Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. I. Multiple effectors act to modulate Okazaki fragment size." J Biol Chem 267(6);4030-44. PMID: 1740451
Wyman93: Wyman C, Vasilikiotis C, Ang D, Georgopoulos C, Echols H (1993). "Function of the GrpE heat shock protein in bidirectional unwinding and replication from the origin of phage lambda." J Biol Chem 268(33);25192-6. PMID: 8227083
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