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Escherichia coli K-12 substr. MG1655 Enzyme: replicative DNA helicase



Gene: dnaB Accession Numbers: EG10236 (EcoCyc), b4052, ECK4044

Synonyms: groP, grpA, grpD

Regulation Summary Diagram: ?

Component of: primosome (summary available)

Subunit composition of replicative DNA helicase = [DnaB]6

Summary:
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].

Locations: cytosol

Map Position: [4,262,337 -> 4,263,752] (91.87 centisomes)
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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006260 - DNA replication Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Hasunuma79]
GO:0006268 - DNA unwinding involved in DNA replication Inferred from experiment [LeBowitz86]
GO:0010212 - response to ionizing radiation Inferred from experiment [Byrne14a]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003678 - DNA helicase activity Inferred from experiment Inferred by computational analysis [GOA01a, LeBowitz86]
GO:0004386 - helicase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, LeBowitz86]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, AriasPalomo13, Ng96, MakowskaGrzyska10, Guy09, Butland05, Mitkova03, Gao01, Seitz00]
GO:0042802 - identical protein binding Inferred from experiment [Bujalowski94, Mitkova03]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for dnaB knockouts: ?

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

a supercoiled duplex DNA + ATP <=> a single stranded DNA + ADP + phosphate

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)

Summary:
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.


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 200 -> 467
[UniProt09]
UniProt: SF4 helicase;
Nucleotide-Phosphate-Binding-Region 231 -> 238
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: probable;
DNA-Binding-Region 324 -> 329
[Biswas99a]
This sequence is required for ssDNA binding, helicase function and the DNA-dependence of DnaB ATPase activity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4052 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10236; confirmed by SwissProt match.


References

Alfano89: Alfano C, McMacken R (1989). "Ordered assembly of nucleoprotein structures at the bacteriophage lambda replication origin during the initiation of DNA replication." J Biol Chem 264(18);10699-708. PMID: 2525129

Allen91: Allen GC, Kornberg A (1991). "Fine balance in the regulation of DnaB helicase by DnaC protein in replication in Escherichia coli." J Biol Chem 266(33);22096-101. PMID: 1657989

Arai81: Arai K, Kornberg A (1981). "Mechanism of dnaB protein action. II. ATP hydrolysis by dnaB protein dependent on single- or double-stranded DNA." J Biol Chem 256(10);5253-9. PMID: 6262325

Arai81a: Arai K, Kornberg A (1981). "Mechanism of dnaB protein action. III. Allosteric role of ATP in the alteration of DNA structure by dnaB protein in priming replication." J Biol Chem 256(10);5260-6. PMID: 6262326

Arai81b: Arai K, Yasuda S, Kornberg A (1981). "Mechanism of dnaB protein action. I. Crystallization and properties of dnaB protein, an essential replication protein in Escherichia coli." J Biol Chem 256(10);5247-52. PMID: 6262324

AriasPalomo13: Arias-Palomo E, O'Shea VL, Hood IV, Berger JM (2013). "The bacterial DnaC helicase loader is a DnaB ring breaker." Cell 153(2);438-48. PMID: 23562643

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Baker87: Baker TA, Funnell BE, Kornberg A (1987). "Helicase action of dnaB protein during replication from the Escherichia coli chromosomal origin in vitro." J Biol Chem 262(14);6877-85. PMID: 3032979

Barcena01: Barcena M, Ruiz T, Donate LE, Brown SE, Dixon NE, Radermacher M, Carazo JM (2001). "The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel." EMBO J 20(6);1462-8. PMID: 11250911

Biswas02: Biswas EE, Chen PH, Biswas SB (2002). "Modulation of enzymatic activities of Escherichia coli DnaB helicase by single-stranded DNA-binding proteins." Nucleic Acids Res 30(13);2809-16. PMID: 12087164

Biswas86: Biswas EE, Biswas SB, Bishop JE (1986). "The dnaB protein of Escherichia coli: mechanism of nucleotide binding, hydrolysis, and modulation by dnaC protein." Biochemistry 25(23);7368-74. PMID: 3026453

Biswas87: Biswas SB, Biswas EE (1987). "Regulation of dnaB function in DNA replication in Escherichia coli by dnaC and lambda P gene products." J Biol Chem 262(16);7831-8. PMID: 3034907

Biswas94: Biswas SB, Chen PH, Biswas EE (1994). "Structure and function of Escherichia coli DnaB protein: role of the N-terminal domain in helicase activity." Biochemistry 33(37);11307-14. PMID: 7727381

Biswas99: Biswas EE, Biswas SB (1999). "Mechanism of DnaB helicase of Escherichia coli: structural domains involved in ATP hydrolysis, DNA binding, and oligomerization." Biochemistry 38(34);10919-28. PMID: 10460147

Biswas99a: Biswas EE, Biswas SB (1999). "Mechanism of DNA binding by the DnaB helicase of Escherichia coli: analysis of the roles of domain gamma in DNA binding." Biochemistry 38(34);10929-39. PMID: 10460148

Bujalowski00: Bujalowski W, Jezewska MJ (2000). "Kinetic mechanism of nucleotide cofactor binding to Escherichia coli replicative helicase DnaB protein. stopped-flow kinetic studies using fluorescent, ribose-, and base-modified nucleotide analogues." Biochemistry 39(8);2106-22. PMID: 10684661

Bujalowski00a: Bujalowski W, Jezewska MJ (2000). "Kinetic mechanism of the single-stranded DNA recognition by Escherichia coli replicative helicase DnaB protein. Application of the matrix projection operator technique to analyze stopped-flow kinetics." J Mol Biol 295(4);831-52. PMID: 10656794

Bujalowski94: Bujalowski W, Klonowska MM, Jezewska MJ (1994). "Oligomeric structure of Escherichia coli primary replicative helicase DnaB protein." J Biol Chem 269(50);31350-8. PMID: 7989299

Bujalowski94a: Bujalowski W, Klonowska MM (1994). "Structural characteristics of the nucleotide-binding site of Escherichia coli primary replicative helicase DnaB protein. Studies with ribose and base-modified fluorescent nucleotide analogs." Biochemistry 33(15);4682-94. PMID: 8161526

Bujalowski95: Bujalowski W, Jezewska MJ (1995). "Interactions of Escherichia coli primary replicative helicase DnaB protein with single-stranded DNA. The nucleic acid does not wrap around the protein hexamer." Biochemistry 34(27);8513-9. PMID: 7612593

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Byrne14a: Byrne RT, Klingele AJ, Cabot EL, Schackwitz WS, Martin JA, Martin J, Wang Z, Wood EA, Pennacchio C, Pennacchio LA, Perna NT, Battista JR, Cox MM (2014). "Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair." Elife 3;e01322. PMID: 24596148

Carr01: Carr KM, Kaguni JM (2001). "Stoichiometry of DnaA and DnaB protein in initiation at the Escherichia coli chromosomal origin." J Biol Chem 276(48);44919-25. PMID: 11551962

Carr02: Carr KM, Kaguni JM (2002). "Escherichia coli DnaA protein loads a single DnaB helicase at a DnaA box hairpin." J Biol Chem 277(42);39815-22. PMID: 12161435

Conrad79: Conrad SE, Campbell JL (1979). "Characterization of an improved in vitro DNA replication system for Escherichia coli plasmids." Nucleic Acids Res 6(10);3289-304. PMID: 384367

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dodson85: Dodson M, Roberts J, McMacken R, Echols H (1985). "Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: complexes with lambda O protein and with lambda O, lambda P, and Escherichia coli DnaB proteins." Proc Natl Acad Sci U S A 82(14);4678-82. PMID: 2991888

Dodson86: Dodson M, Echols H, Wickner S, Alfano C, Mensa-Wilmot K, Gomes B, LeBowitz J, Roberts JD, McMacken R (1986). "Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: localized unwinding of duplex DNA by a six-protein reaction." Proc Natl Acad Sci U S A 83(20);7638-42. PMID: 3020552

Donate00: Donate LE, Llorca O, Barcena M, Brown SE, Dixon NE, Carazo JM (2000). "pH-controlled quaternary states of hexameric DnaB helicase." J Mol Biol 303(3);383-93. PMID: 11031115

Doran98: Doran KS, Konieczny I, Helinski DR (1998). "Replication origin of the broad host range plasmid RK2. Positioning of various motifs is critical for initiation of replication." J Biol Chem 273(14);8447-53. PMID: 9525957

Fass99: Fass D, Bogden CE, Berger JM (1999). "Crystal structure of the N-terminal domain of the DnaB hexameric helicase." Structure Fold Des 7(6);691-8. PMID: 10404598

Flowers03: Flowers S, Biswas EE, Biswas SB (2003). "Conformational dynamics of DnaB helicase upon DNA and nucleotide binding: analysis by intrinsic tryptophan fluorescence quenching." Biochemistry 42(7);1910-21. PMID: 12590577

Fujimura79: Fujimura FK, Zyskind JW, Smith DW (1979). "The Escherichia coli dnaB protein is required for initiation of chromosomal DNA replication." Cold Spring Harb Symp Quant Biol 43 Pt 1;559-62. PMID: 383382

Funnell86: Funnell BE, Baker TA, Kornberg A (1986). "Complete enzymatic replication of plasmids containing the origin of the Escherichia coli chromosome." J Biol Chem 261(12);5616-24. PMID: 3514619

Funnell87: Funnell BE, Baker TA, Kornberg A (1987). "In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome." J Biol Chem 262(21);10327-34. PMID: 3038874

Galletto03: Galletto R, Jezewska MJ, Bujalowski W (2003). "Interactions of the Escherichia coli DnaB helicase hexamer with the replication factor the DnaC protein. Effect of nucleotide cofactors and the ssDNA on protein-protein interactions and the topology of the complex." J Mol Biol 329(3);441-65. PMID: 12767828

Galletto04: Galletto R, Jezewska MJ, Bujalowski W (2004). "Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DnaB helicase using rapid quench-flow method." J Mol Biol 343(1);83-99. PMID: 15381422

Galletto04a: Galletto R, Jezewska MJ, Bujalowski W (2004). "Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3' arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase." J Mol Biol 343(1);101-14. PMID: 15381423

Gao01: Gao D, McHenry CS (2001). "tau binds and organizes Escherichia coli replication proteins through distinct domains. Domain IV, located within the unique C terminus of tau, binds the replication fork, helicase, DnaB." J Biol Chem 276(6);4441-6. PMID: 11078744

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Guy09: Guy CP, Atkinson J, Gupta MK, Mahdi AA, Gwynn EJ, Rudolph CJ, Moon PB, van Knippenberg IC, Cadman CJ, Dillingham MS, Lloyd RG, McGlynn P (2009). "Rep provides a second motor at the replisome to promote duplication of protein-bound DNA." Mol Cell 36(4);654-66. PMID: 19941825

Hasunuma79: Hasunuma K, Sekiguchi M (1979). "Effect of dna mutations on the replication of plasmid pSC101 in Escherichia coli K-12." J Bacteriol 137(3);1095-9. PMID: 374337

Heller05: Heller RC, Marians KJ (2005). "The disposition of nascent strands at stalled replication forks dictates the pathway of replisome loading during restart." Mol Cell 17(5);733-43. PMID: 15749022

Hiasa92: Hiasa H, Marians KJ (1992). "Differential inhibition of the DNA translocation and DNA unwinding activities of DNA helicases by the Escherichia coli Tus protein." J Biol Chem 267(16);11379-85. PMID: 1317865

Hiasa99: Hiasa H, Marians KJ (1999). "Initiation of bidirectional replication at the chromosomal origin is directed by the interaction between helicase and primase." J Biol Chem 274(38);27244-8. PMID: 10480943

Jezewska96: Jezewska MJ, Bujalowski W (1996). "Global conformational transitions in Escherichia coli primary replicative helicase DnaB protein induced by ATP, ADP, and single-stranded DNA binding. Multiple conformational states of the helicase hexamer." J Biol Chem 271(8);4261-5. PMID: 8626772

Jezewska96a: Jezewska MJ, Kim US, Bujalowski W (1996). "Binding of Escherichia coli primary replicative helicase DnaB protein to single-stranded DNA. Long-range allosteric conformational changes within the protein hexamer." Biochemistry 35(7);2129-45. PMID: 8652555

Jezewska97: Jezewska MJ, Rajendran S, Bujalowski W (1997). "Strand specificity in the interactions of Escherichia coli primary replicative helicase DnaB protein with a replication fork." Biochemistry 36(33);10320-6. PMID: 9254631

Jezewska98: Jezewska MJ, Rajendran S, Bujalowska D, Bujalowski W (1998). "Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli DnaB Helicase? Fluorescence energy transfer studies." J Biol Chem 273(17);10515-29. PMID: 9553111

Jezewska98a: Jezewska MJ, Rajendran S, Bujalowski W (1998). "Complex of Escherichia coli primary replicative helicase DnaB protein with a replication fork: recognition and structure." Biochemistry 37(9);3116-36. PMID: 9485465

Jezewska98b: Jezewska MJ, Rajendran S, Bujalowski W (1998). "Functional and structural heterogeneity of the DNA binding site of the Escherichia coli primary replicative helicase DnaB protein." J Biol Chem 273(15);9058-69. PMID: 9535894

Johnson00: Johnson SK, Bhattacharyya S, Griep MA (2000). "DnaB helicase stimulates primer synthesis activity on short oligonucleotide templates." Biochemistry 39(4);736-44. PMID: 10651639

Johnson75: Johnson RC (1975). "Postreplication repair gap filling in an Escherichia coli strain deficient in dnaB gene product." Basic Life Sci 5A;325-9. PMID: 1103841

Jones99: Jones JM, Nakai H (1999). "Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate." J Mol Biol 289(3);503-16. PMID: 10356325

Kaguni85: Kaguni JM, Bertsch LL, Bramhill D, Flynn JE, Fuller RS, Funnell B, Maki S, Ogawa T, Ogawa K, van der Ende A (1985). "Initiation of replication of the Escherichia coli chromosomal origin reconstituted with purified enzymes." Basic Life Sci 30;141-50. PMID: 2990405

Kaplan02: Kaplan DL, O'Donnell M (2002). "DnaB drives DNA branch migration and dislodges proteins while encircling two DNA strands." Mol Cell 10(3);647-57. PMID: 12408831

Kaplan04: Kaplan DL, O'Donnell M (2004). "Twin DNA pumps of a hexameric helicase provide power to simultaneously melt two duplexes." Mol Cell 15(3);453-65. PMID: 15304224

LeBowitz86: LeBowitz JH, McMacken R (1986). "The Escherichia coli dnaB replication protein is a DNA helicase." J Biol Chem 261(10);4738-48. PMID: 3007474

Lee89: Lee EH, Kornberg A, Hidaka M, Kobayashi T, Horiuchi T (1989). "Escherichia coli replication termination protein impedes the action of helicases." Proc Natl Acad Sci U S A 86(23);9104-8. PMID: 2556700

Liberek90: Liberek K, Osipiuk J, Zylicz M, Ang D, Skorko J, Georgopoulos C (1990). "Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication." J Biol Chem 265(6);3022-9. PMID: 2154468

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lovett02: Lovett ST, Hurley RL, Sutera VA, Aubuchon RH, Lebedeva MA (2002). "Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways." Genetics 160(3);851-9. PMID: 11901106

Lu96: Lu YB, Ratnakar PV, Mohanty BK, Bastia D (1996). "Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA." Proc Natl Acad Sci U S A 93(23);12902-7. PMID: 8917517

MakowskaGrzyska10: Makowska-Grzyska M, Kaguni JM (2010). "Primase directs the release of DnaC from DnaB." Mol Cell 37(1);90-101. PMID: 20129058

Mallory90: Mallory JB, Alfano C, McMacken R (1990). "Host virus interactions in the initiation of bacteriophage lambda DNA replication. Recruitment of Escherichia coli DnaB helicase by lambda P replication protein." J Biol Chem 265(22);13297-307. PMID: 2165499

Marszalek94: Marszalek J, Kaguni JM (1994). "DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli." J Biol Chem 269(7);4883-90. PMID: 8106460

McMacken77: McMacken R, Ueda K, Kornberg A (1977). "Migration of Escherichia coli dnaB protein on the template DNA strand as a mechanism in initiating DNA replication." Proc Natl Acad Sci U S A 74(10);4190-4. PMID: 144914

Michel97: Michel B, Ehrlich SD, Uzest M (1997). "DNA double-strand breaks caused by replication arrest." EMBO J 16(2);430-8. PMID: 9029161

Miles97: Miles CS, Weigelt J, Stamford NP, Dammerova N, Otting G, Dixon NE (1997). "Precise limits of the N-terminal domain of DnaB helicase determined by NMR spectroscopy." Biochem Biophys Res Commun 231(1);126-30. PMID: 9070233

Mitkova03: Mitkova AV, Khopde SM, Biswas SB (2003). "Mechanism and stoichiometry of interaction of DnaG primase with DnaB helicase of Escherichia coli in RNA primer synthesis." J Biol Chem 278(52);52253-61. PMID: 14557266

Mulugu01: Mulugu S, Potnis A, Shamsuzzaman , Taylor J, Alexander K, Bastia D (2001). "Mechanism of termination of DNA replication of Escherichia coli involves helicase-contrahelicase interaction." Proc Natl Acad Sci U S A 98(17);9569-74. PMID: 11493686

Nakayama84: Nakayama N, Arai N, Kaziro Y, Arai K (1984). "Structural and functional studies of the dnaB protein using limited proteolysis. Characterization of domains for DNA-dependent ATP hydrolysis and for protein association in the primosome." J Biol Chem 259(1);88-96. PMID: 6323419

Natarajan93: Natarajan S, Kaul S, Miron A, Bastia D (1993). "A 27 kd protein of E. coli promotes antitermination of replication in vitro at a sequence-specific replication terminus." Cell 72(1);113-20. PMID: 8380756

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

Ng96a: Ng JY, Marians KJ (1996). "The ordered assembly of the phiX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes." J Biol Chem 271(26);15642-8. PMID: 8663104

Pritchard80: Pritchard JJ, Rowbury RJ (1980). "Host components required for the replication of the resistance plasmid R124 and a copy mutant derivative." Z Allg Mikrobiol 20(2);129-40. PMID: 6990641

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Rajendran00: Rajendran S, Jezewska MJ, Bujalowski W (2000). "Multiple-step kinetic mechanism of DNA-independent ATP binding and hydrolysis by Escherichia coli replicative helicase DnaB protein: quantitative analysis using the rapid quench-flow method." J Mol Biol 303(5);773-95. PMID: 11061975

RehaKrantz78: Reha-Krantz LJ, Hurwitz J (1978). "The dnaB gene product of Escherichia coli. I. Purification, homogeneity, and physical properties." J Biol Chem 253(11);4043-50. PMID: 206559

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

Saveson97: Saveson CJ, Lovett ST (1997). "Enhanced deletion formation by aberrant DNA replication in Escherichia coli." Genetics 146(2);457-70. PMID: 9177997

Seitz00: Seitz H, Weigel C, Messer W (2000). "The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli." Mol Microbiol 37(5);1270-9. PMID: 10972842

Skarstad95: Skarstad K, Wold S (1995). "The speed of the Escherichia coli fork in vivo depends on the DnaB:DnaC ratio." Mol Microbiol 17(5);825-31. PMID: 8596432

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

Stordal96: Stordal L, Maurer R (1996). "Defect in general priming conferred by linker region mutants of Escherichia coli dnaB." J Bacteriol 178(15);4620-7. PMID: 8755893

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

Tougu96: Tougu K, Marians KJ (1996). "The interaction between helicase and primase sets the replication fork clock." J Biol Chem 271(35);21398-405. PMID: 8702921

Ueda78: Ueda K, McMacken R, Kornberg A (1978). "dnaB protein of Escherichia coli. Purification and role in the replication of phiX174 DNA." J Biol Chem 253(1);261-9. PMID: 145439

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Wahle89a: Wahle E, Lasken RS, Kornberg A (1989). "The dnaB-dnaC replication protein complex of Escherichia coli. I. Formation and properties." J Biol Chem 264(5);2463-8. PMID: 2536712

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

Wickner75: Wickner S, Hurwitz J (1975). "Interaction of Escherichia coli dnaB and dnaC(D) gene products in vitro." Proc Natl Acad Sci U S A 72(3);921-5. PMID: 1093174

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

Yamashita99: Yamashita T, Hanada K, Iwasaki M, Yamaguchi H, Ikeda H (1999). "Illegitimate recombination induced by overproduction of DnaB helicase in Escherichia coli." J Bacteriol 181(15);4549-53. PMID: 10419952

YanceyWrona92: Yancey-Wrona JE, Matson SW (1992). "Bound Lac repressor protein differentially inhibits the unwinding reactions catalyzed by DNA helicases." Nucleic Acids Res 20(24);6713-21. PMID: 1336182

Yang02: Yang S, Yu X, VanLoock MS, Jezewska MJ, Bujalowski W, Egelman EH (2002). "Flexibility of the rings: structural asymmetry in the DnaB hexameric helicase." J Mol Biol 321(5);839-49. PMID: 12206765

Yoda91: Yoda K, Okazaki T (1991). "Specificity of recognition sequence for Escherichia coli primase." Mol Gen Genet 227(1);1-8. PMID: 1828532

Yu96: Yu X, Jezewska MJ, Bujalowski W, Egelman EH (1996). "The hexameric E. coli DnaB helicase can exist in different Quaternary states." J Mol Biol 259(1);7-14. PMID: 8648650

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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