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discounted EARLY registration ends Dec 31, 2014
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12/28 - 12/31
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
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Escherichia coli K-12 substr. MG1655 Protein: 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 [Ng96]. Despite its absence from this model of ordered assembly, PriC is also found in isolated intact primosomes [Ng96a]. Note that the primosome components have many functions in the cell that do not require the full primosome.

Gene-Reaction Schematic: ?


Component enzyme of primosome : replicative DNA helicase

Synonyms: groP, grpA, grpD

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

Locations: cytosol

Subunit composition of replicative DNA helicase = [DnaB]6

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]

GO Terms:

Biological Process: GO:0006260 - DNA replication Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, 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 [UniProtGOA11]
Molecular Function: GO:0003678 - DNA helicase activity Inferred from experiment Inferred by computational analysis [GOA01, LeBowitz86]
GO:0004386 - helicase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, LeBowitz86]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, AriasPalomo13, Ng96a, MakowskaGrzyska10, Guy09, Butland05, Mitkova03, Gao01a, Seitz00]
GO:0042802 - identical protein binding Inferred from experiment [Bujalowski94, Mitkova03]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Unification Links: DIP:DIP-35913N , EcoliWiki:b4052 , Mint:MINT-584605 , ModBase:P0ACB0 , PR:PRO_000022460 , Pride:P0ACB0 , Protein Model Portal:P0ACB0 , RefSeq:NP_418476 , 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

Catalyzes:
a supercoiled duplex DNA + ATP = a single stranded DNA + ADP + phosphate

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, Carr02a]. 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 [Wu92c].

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 [Jones99a]. 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) [Lu96a]. 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 [Johnson00a]. 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, Arai81a]. 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 [Arai81b, 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, Arai81c]. 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, Yang02c]. 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 [Lee89a, 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].

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]

Subunit of primosome: primosomal protein DnaT

Synonyms: primosomal protein i

Gene: dnaT Accession Numbers: EG10244 (EcoCyc), b4362, ECK4352

Locations: cytosol

Subunit composition of primosomal protein DnaT = [DnaT]3
         primosomal protein DnaT = DnaT

Map Position: [4,599,001 <- 4,599,540] (99.12 centisomes)
Length: 540 bp / 179 aa

Molecular Weight of Polypeptide: 19.455 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006261 - DNA-dependent DNA replication Inferred from experiment [Lark78]
GO:0006267 - pre-replicative complex assembly involved in nuclear cell cycle DNA replication Inferred from experiment [Liu96b]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Lopper07]
Cellular Component: GO:0005829 - cytosol
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Unification Links: DIP:DIP-47957N , EcoliWiki:b4362 , Mint:MINT-1256745 , PR:PRO_000022468 , Protein Model Portal:P0A8J2 , RefSeq:NP_418782 , String:511145.b4362 , UniProt:P0A8J2

Relationship Links: InterPro:IN-FAMILY:IPR020917

Summary:
DnaT is required for chromosomal DNA replication and for induction of replication in the absence of protein synthesis during the SOS response [Lark78, Masai86]. Though its precise role in cellular DNA replication is unknown, DnaT is a required component of the primosome, a complex of proteins capable of priming phiX174 DNA replication in vitro, and suspected of being involved in the restart of stalled replication forks in vivo [Arai81d, Allen93]. DnaT complexes with PriA during primosome formation [Liu96b]. DnaT appears to be specifically required for primosome function when replication stalls with a leading nascent strand rather than a gapped fork [Heller05].

DnaT is required for replication of plasmid pBR322 in vivo and in vitro, being specifically necessary for synthesis on the lagging strand [Masai89, Masai88]. It is also necessary for plasmid RSF1010 replication, and for rolling-circle replication of plasmid DNA generally [Scherzinger91, Allen93a]. It is not, however, needed for plasmid R1 replication either in vivo or in vitro [Masai89].

When overexpressed, dnaT is a mutator gene [Yang04].

DnaT unfolding has been studied [Antony96].

Gene Citations: [Masai88a]

Essentiality data for dnaT knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of primosome: primosomal replication protein N

Gene: priB Accession Numbers: EG10764 (EcoCyc), b4201, ECK4197

Locations: cytosol

Subunit composition of primosomal replication protein N = [PriB]2

Map Position: [4,423,543 -> 4,423,857] (95.34 centisomes)
Length: 315 bp / 104 aa

Molecular Weight of Polypeptide: 11.442 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006270 - DNA replication initiation Inferred from experiment [Sandler05]
GO:0006276 - plasmid maintenance Inferred from experiment [Berges97]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003697 - single-stranded DNA binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Low82]
GO:0005515 - protein binding Inferred from experiment [Lopper07]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0030894 - replisome Inferred by computational analysis [GOA01]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Unification Links: DIP:DIP-10563N , EcoliWiki:b4201 , ModBase:P07013 , PR:PRO_000023592 , Protein Model Portal:P07013 , RefSeq:NP_418622 , SMR:P07013 , String:511145.b4201 , UniProt:P07013

Relationship Links: InterPro:IN-FAMILY:IPR000424 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR023646 , PDB:Structure:1TXY , PDB:Structure:1TXY , PDB:Structure:1V1Q , PDB:Structure:1V1Q , PDB:Structure:1WOC , PDB:Structure:1WOC , PDB:Structure:2CCZ , PDB:Structure:2CCZ , PDB:Structure:2PNH , Pfam:IN-FAMILY:PF00436 , Prosite:IN-FAMILY:PS50935

Summary:
PriB is a component of the primosome, a multiprotein complex that is believed to be involved in restart of stalled replication forks. Based on genetic studies, some PriA-dependent restart pathways require PriB [Sandler00]. Other research shows that a pathway dependent on both PriA and PriB is used when stalled replication forks have no leading strand gaps, alternately turning to a PriC pathway when there are large gaps [Heller05].

PriB is a core component of the primosome, binding to PriA and single-stranded DNA (ssDNA) shortly after PriA binds DNA, stabilizing the PriA-DNA interaction [Ng96, Allen93]. PriB also assists in subsequent binding of DnaT to PriA [Liu96b]. In the case of phiX174 phage, PriB interacts directly with single-strand binding protein (SSB) [Low82]. While it is bound, PriB stimulates the helicase activity and processivity of PriA [Cadman05].

Several crystal structures have been determined for PriB, all to around 2 Å resolution. Based on these structures, PriB exists as a dimer and is very structurally similar to SSB [Shioi05, Lopper04, Liu04e]. Based on sequence comparison and operon organization PriB appears to have evolved from SSB via gene duplication [Ponomarev03]. A 2.7 Å-resolution crystal structure of PriB complexed with a short oligo shows that although PriB is structurally similar to SSB, it binds ssDNA differently [Huang06c]. By shift assay, PriB binds both ssDNA and ssRNA equally well [Liu04e].

PriB is required for "constitutive stable DNA replication," that is DNA replication that occurs in the absence of protein synthesis in an rnha mutant [Sandler05].

Though priB nulls have very little phenotypic effect, priBC double nulls demonstrate slow growth and reduced viability [Sandler99]. Certain priB mutants are also deficient in maintenance of some kinds of plasmids [Berges97].

Citations: [Allen91a, Zavitz91]

Gene Citations: [Allen91a]

Essentiality data for priB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Subunit of primosome: primosome factor N'

Synonyms: SrgA, replication factor Y, PriA

Gene: priA Accession Numbers: EG10763 (EcoCyc), b3935, ECK3927

Locations: cytosol

Sequence Length: 732 AAs

Molecular Weight: 81.655 kD (from nucleotide sequence)

Molecular Weight: 78 kD (experimental) [Nurse90]

GO Terms:

Biological Process: GO:0006260 - DNA replication Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Rangarajan02]
GO:0006261 - DNA-dependent DNA replication Inferred from experiment [Liu99c]
GO:0006268 - DNA unwinding involved in DNA replication Inferred from experiment [Lee87a]
GO:0006270 - DNA replication initiation Inferred from experiment [Masai94]
GO:0006276 - plasmid maintenance Inferred from experiment [Lee91a]
GO:0006302 - double-strand break repair Inferred from experiment [Kogoma96]
GO:0006310 - DNA recombination Inferred from experiment [Kogoma96]
GO:0010332 - response to gamma radiation Inferred from experiment [Kogoma96]
GO:0046677 - response to antibiotic Inferred from experiment [Kogoma96]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004386 - helicase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Lee87a]
GO:0005515 - protein binding Inferred from experiment [Kozlov10, Lopper07]
GO:0043140 - ATP-dependent 3'-5' DNA helicase activity Inferred from experiment [Lee90a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Unification Links: DIP:DIP-10562N , EcoliWiki:b3935 , Mint:MINT-1274231 , ModBase:P17888 , PR:PRO_000023591 , Protein Model Portal:P17888 , RefSeq:NP_418370 , SMR:P17888 , String:511145.b3935 , UniProt:P17888

Relationship Links: InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR005259 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2D7E , PDB:Structure:2D7G , PDB:Structure:2D7H , PDB:Structure:2DWL , PDB:Structure:2DWM , PDB:Structure:2DWN , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF00271 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490

Summary:
The role of PriA in the cell appears to be the restart of stalled replication forks. PriA, along with DNA polymerase II, is required to restart DNA synthesis immediately following UV exposure [Rangarajan02]. Based on genetic interactions, there seem to be two replication restart pathways that require PriA, one using RecG, the other using RuvABC [Meddows04, Gregg02].

PriA binds to the 3' terminus of nascent DNA at stalled replication forks in vitro, leading to assembly of the full primosome at the binding site [Mizukoshi03]. PriA preferentially binds to stalled forks with D loops, which are intermediates in recombination-based recovery from a stall [Liu99c, McGlynn97]. Larger single-stranded gaps at the stall site favor PriC-mediated restart rather than PriA involvement [Heller05]. PriA binding is most effective when the lagging strand is duplex and the leading strand is single stranded [Jones01]. D loop binding leads to assembly of the full primosome at the stall site [Liu99d].

In many plasmids and phages, PriA and the primosome function in initiation of normal DNA replication. In this context, PriA binds to the primosome assembly site (PAS), a double-hairpin DNA structure that acts as the origin of replication for replicative DNA synthesis [Greenbaum85, Soeller82, Zipursky81, Zipursky80, Allen93, Jones99a]. Following PAS binding, PriA translocates 3' to 5' along ssDNA in an ATP-dependent fashion, after which it can move onto and unwind duplex DNA, a process that also uses ATP [Lee90a, Lee87a]. This PriA-mediated unwinding moves just as fast as unwinding catalyzed by the normal replicative helicase, DnaB, and is stimulated by interaction with single-strand binding protein (SSB) via the SSB carboxy-terminus [Mok87, Cadman04]. PriA helicase activity is blocked by Tus bound at ter replication termination sites [Hiasa92, Lee92d].

PriA binding is the first step in assembly of the primosome, a multiprotein complex that restarts stalled replication forks in E. coli and initiates replication in various plasmids and phages [Ng96]. The primosomal protein PriB helps PriA bind DnaT, as well as stimulating the processivity and helicase activity of PriA [Liu96b, Cadman05]. PriA activity doubles in the completed primosome [Allen93]. Notably, PriA that lacks its helicase and translocation activities can still catalyze primosome assembly, and this alone appears to be sufficient to correct defects in homologous recombination and double-strand-break repair that are normally present in priA null mutants [Zavitz92, Kogoma96].

PriA binds ssDNA as a monomer via a single DNA-binding site, binding to as few as 8 nucleotides [Jezewska00, Jezewska00a]. This binding occurs in the PriA amino-terminal domain, though the helicase domain works together with it synergistically to allow high-affinity binding of D loops at replication forks [Tanaka02a, Chen04b]. Helicase activity is not required for this binding [Tanaka03]. The kinetics of PriA binding to ssDNA have been examined in detail [Galletto04b].

The amino-terminal domain of PriA has been crystallized [Sasaki06].

PriA is required for inducible and constitutive stable DNA replication in the absence of protein synthesis [Masai94].

priA null mutants are unable to generate phiX174 phage or maintain plasmids that use an E. coli origin of replication. They also have growth defects and a filamentous phenotype [Lee91a]. The SOS response is induced in these mutants [Nurse91]. Loss of PriA helicase activity suppresses the deleterious effects of the loss of RecG recombinational helicase function [AlDeib96].

Citations: [Wickner75a, Lee90, Ouzounis91]

Essentiality data for priA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of primosome: primosomal replication protein N''

Synonyms: PriC

Gene: priC Accession Numbers: EG10765 (EcoCyc), b0467, ECK0461

Locations: cytosol

Sequence Length: 175 AAs

Molecular Weight: 20.375 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006261 - DNA-dependent DNA replication Inferred from experiment [Sandler00]
GO:0006270 - DNA replication initiation Inferred from experiment [Ng96a]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Heller05]
GO:0005515 - protein binding Inferred from experiment [Ng96a, Rajagopala14]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Unification Links: DIP:DIP-10564N , EcoliWiki:b0467 , PR:PRO_000023593 , Pride:P23862 , Protein Model Portal:P23862 , RefSeq:NP_415000 , String:511145.b0467 , UniProt:P23862

Relationship Links: InterPro:IN-FAMILY:IPR010890 , PDB:Structure:2RT6 , Pfam:IN-FAMILY:PF07445

Summary:
PriC is part of the primosome, a protein complex believed to be required for restart of stalled replication forks [Masai90]. As a primosome component, PriC binds after the PriA-PriB-DNA complex forms [Allen93]. Though PriC does not contribute to the stability of the PriA-PriB-DNA complex, in its absence from the phiX174 replication model, priming drops by one third and replication by one half [Ng96].

Based on genetic studies, stalled replication forks can restart via a mechanism requiring PriA and either PriB or PriC, or with PriC and Rep instead of PriA [Sandler00]. Whereas PriA-dependent restart occurs when there are no gaps in the leading strand, PriC-dependent restart requires a gap [Heller05]. This can be blocked if the 5' end of the lagging strand is near the replication fork, requiring the unwinding activity of Rep or PriA to allow PriC-mediated restart [Heller05a]. PriC in turn stimulates Rep activity at stalled forks [Heller05a].

A priC has limited phenotype, but a priBC double null suffers a large reduction in growth and viability [Sandler99].

Citations: [Zavitz91]

Essentiality data for priC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Component enzyme of primosome : DNA primase

Synonyms: SdgA, ParB, DnaP, DnaG

Gene: dnaG Accession Numbers: EG10239 (EcoCyc), b3066, ECK3056

Locations: cytosol

Sequence Length: 581 AAs

Molecular Weight: 65.565 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006269 - DNA replication, synthesis of RNA primer Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Rowen78]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0003896 - DNA primase activity Inferred from experiment Inferred by computational analysis [GOA01, Rowen78]
GO:0005515 - protein binding Inferred from experiment [Yuzhakov99, Ng96a, Mitkova03]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA01, Stamford92]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003899 - DNA-directed RNA polymerase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Rowen78]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Unification Links: DIP:DIP-47954N , EcoliWiki:b3066 , Mint:MINT-1222307 , ModBase:P0ABS5 , PR:PRO_000022463 , Pride:P0ABS5 , Protein Model Portal:P0ABS5 , RefSeq:NP_417538 , SMR:P0ABS5 , String:511145.b3066 , UniProt:P0ABS5

Relationship Links: InterPro:IN-FAMILY:IPR002694 , InterPro:IN-FAMILY:IPR006171 , InterPro:IN-FAMILY:IPR006295 , InterPro:IN-FAMILY:IPR013173 , InterPro:IN-FAMILY:IPR013264 , InterPro:IN-FAMILY:IPR016136 , InterPro:IN-FAMILY:IPR019475 , PDB:Structure:1DD9 , PDB:Structure:1DDE , PDB:Structure:1EQN , PDB:Structure:1T3W , PDB:Structure:2HAJ , PDB:Structure:3B39 , Pfam:IN-FAMILY:PF01807 , Pfam:IN-FAMILY:PF08275 , Pfam:IN-FAMILY:PF08278 , Pfam:IN-FAMILY:PF10410 , Pfam:IN-FAMILY:PF13662 , Prosite:IN-FAMILY:PS50880 , Smart:IN-FAMILY:SM00400 , Smart:IN-FAMILY:SM00493 , Smart:IN-FAMILY:SM00766

Catalyzes:
a single stranded DNA = a short RNA Segment

Summary:
DNA primase catalyzes the synthesis of RNA primers on single-stranded template DNA [Rowen78]. These primers then serve as the starting point for DNA synthesis by DNA polymerase III [Bouche75].

Using single-stranded DNA in vitro, primase and NTPs are sufficient to produce RNA primers [Swart93, vanderEnde85, Swart95]. In practice, primase also relies on ssDNA-binding protein (SSB) to stabilize its interaction with the primer. The Chi subunit of DNA polymerase III interacts with SSB near the primer, displacing DNA primase and allowing loading of the DNA polymerase III beta sliding clamp [Yuzhakov99, Sun98]. Primase binds three distinct sites during priming, one of them as far as 115 nucleotides distant from the start of primer synthesis [Sims80]. In the case of lagging strand synthesis, primase dissociates from DNA each time an Okazaki fragment is completed and then repeats this binding process to begin priming of the next fragment [Wu92c].

During replication, primase follows DNA helicase as the helicase processively unwinds DNA at the replication fork, putting down primers on the lagging strand in its wake [McMacken77]. Three DnaG monomers bind per helicase hexamer via the DnaG carboxy-terminal domain [Oakley05]. This physical interaction is required for optimal primer synthesis, stimulating primase function 5,000 fold [Lu96a, Zhang02g, Johnson00a]. In addition, interaction with helicase reduces the specificity of the primer initiation site from CTG to PyPyPu [Bhattacharyya00, Yoda91]. The degree of interaction between primase and helicase sets the length of Okazaki fragments [Tougu96]. More generally, the availability of primase controls how frequently new fragments are started and thus how long they are, and therefore the ssDNA-binding capability of helicase is required to direct primase to new template DNA [Wu92d, Zechner92a, Mitkova03]. Initiation of bidirectional replication from oriC also requires the helicase-primase interaction, as this controls proper leading-strand primer placement [Hiasa99, Hiasa94]. Primer length is constrained by the addition of DnaC, which loads helicase onto DNA [Mitkova03]. The presence of DNA polymerase III, which follows helicase, also limits primer length to about 10 nucleotides [Zechner92].

Two primases bind at the site of primer initiation, although they do not appear to form a dimer. This differs from the stoichiometry of interaction with helicase discussed above [Khopde02, Stayton83a].

Primase has been subject to structural and cofactor analysis. Its catalytic activity is located in the amino-terminus, although the helicase-interacting carboxy-terminal domain is also required for priming at the replication fork [Tougu94, Loscha04]. The catalytic center has been evaluated by crosslinking as well as via crystal structures at 2.9, 1.7 and 1.6 Å resolution, which reveal that the core has a TOPRIM domain similar to DNA topoisomerases [Mustaev95, Podobnik00, Keck00]. The core catalytic domain contains several metal-coordinating residues [Keck00, Godson00]. Primase appears to bind two magnesium ions and has been shown to contain about one gram of zinc per mol of purified protein [Urlacher95, Stamford92]. Deletion of a putative zinc-binding region in the amino-terminus inactivates primase [Stamford92]. Zinc in primase prevents formation of deleterious disulfide bonds between the cysteines that coordinate the zinc ions [Griep96]. The binding of zinc and the effect of magnesium abundance on zinc binding has been examined in detail [Powers99].

Primase is required for initiation of DNA replication in plasmids and phages. It is a component of the primosome, a complex that initiates DNA replication in phiX174 phage in vitro [Ng96a, Ng96]. Other phages that depend on primase include T4 and alpha 3 [Lilien82, Benz80]. Plasmids that require primase to initiate replication include Mu, R1, mini RK2 and pSC101 [Kruklitis94, Ortega86, Masai89a, Pinkney88, Ely85]. Sequence and structure comparisons have been made across phage and plasmid priming sites [Tanaka94].

In vitro, primase can polymerize RNA from the 3' end of a DNA oligomer primer [Sun98a].

Primase is regulated posttranscriptionally by RNase E, which cleaves its mRNA, and by its use of rare codons, which may serve to keep its expression lower than other cotranscribed genes [Yajnik93, Konigsberg83].

Essentiality data for dnaG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

References

AlDeib96: Al-Deib AA, Mahdi AA, Lloyd RG (1996). "Modulation of recombination and DNA repair by the RecG and PriA helicases of Escherichia coli K-12." J Bacteriol 178(23);6782-9. PMID: 8955297

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

Allen91a: Allen GC, Kornberg A (1991). "The priB gene encoding the primosomal replication n protein of Escherichia coli." J Biol Chem 1991;266(18);11610-3. PMID: 1646811

Allen93: Allen GC, Kornberg A (1993). "Assembly of the primosome of DNA replication in Escherichia coli." J Biol Chem 268(26);19204-9. PMID: 8366072

Allen93a: Allen GC, Dixon NE, Kornberg A (1993). "Strand switching of a replicative DNA helicase promoted by the E. coli primosome." Cell 74(4);713-22. PMID: 8395352

Antony96: Antony T, Kumar S, Chauhan M, Atreyi M, Khatri GS (1996). "Effects of Mg2+ and denaturants on the unfolding pattern of DNA-T--a replication protein of E. coli." Int J Biol Macromol 19(2);91-7. PMID: 8842771

Arai81a: 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

Arai81b: 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

Arai81c: 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

Arai81d: Arai K, McMacken R, Yasuda S, Kornberg A (1981). "Purification and properties of Escherichia coli protein i, a prepriming protein in phi X174 DNA replication." J Biol Chem 256(10);5281-6. PMID: 6453123

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

Benz80: Benz EW, Reinberg D, Vicuna R, Hurwitz J (1980). "Initiation of DNA replication by the dnaG protein." J Biol Chem 255(3);1096-106. PMID: 6985903

Berges97: Berges H, Oreglia J, Joseph-Liauzun E, Fayet O (1997). "Isolation and characterization of a priB mutant of Escherichia coli influencing plasmid copy number of delta rop ColE1-type plasmids." J Bacteriol 179(3);956-8. PMID: 9006055

Bhattacharyya00: Bhattacharyya S, Griep MA (2000). "DnaB helicase affects the initiation specificity of Escherichia coli primase on single-stranded DNA templates." Biochemistry 39(4);745-52. PMID: 10651640

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

Bouche75: Bouche JP, Zechel K, Kornberg A (1975). "dnaG gene product, a rifampicin-resistant RNA polymerase, initiates the conversion of a single-stranded coliphage DNA to its duplex replicative form." J Biol Chem 250(15);5995-6001. PMID: 1097446

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

Cadman04: Cadman CJ, McGlynn P (2004). "PriA helicase and SSB interact physically and functionally." Nucleic Acids Res 32(21);6378-87. PMID: 15576682

Cadman05: Cadman CJ, Lopper M, Moon PB, Keck JL, McGlynn P (2005). "PriB stimulates PriA helicase via an interaction with single-stranded DNA." J Biol Chem 280(48);39693-700. PMID: 16188886

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

Carr02a: 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

Chen04b: Chen HW, North SH, Nakai H (2004). "Properties of the PriA helicase domain and its role in binding PriA to specific DNA structures." J Biol Chem 279(37);38503-12. PMID: 15252043

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

Ely85: Ely S, Wright A (1985). "Maintenance of plasmid pSC101 in Escherichia coli requires the host primase." J Bacteriol 164(1);484-6. PMID: 3900047

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

Galletto04b: Galletto R, Jezewska MJ, Bujalowski W (2004). "Multistep sequential mechanism of Escherichia coli helicase PriA protein-ssDNA interactions. Kinetics and energetics of the active ssDNA-searching site of the enzyme." Biochemistry 43(34);11002-16. PMID: 15323559

Gao01a: 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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Godson00: Godson GN, Schoenich J, Sun W, Mustaev AA (2000). "Identification of the magnesium ion binding site in the catalytic center of Escherichia coli primase by iron cleavage." Biochemistry 39(2);332-9. PMID: 10630993

Greenbaum85: Greenbaum JH, Marians KJ (1985). "Mutational analysis of primosome assembly sites. Evidence for alternative DNA structures." J Biol Chem 260(22);12266-72. PMID: 2931433

Gregg02: Gregg AV, McGlynn P, Jaktaji RP, Lloyd RG (2002). "Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities." Mol Cell 9(2);241-51. PMID: 11864599

Griep96: Griep MA, Lokey ER (1996). "The role of zinc and the reactivity of cysteines in Escherichia coli primase." Biochemistry 35(25);8260-7. PMID: 8679581

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

Heller05a: Heller RC, Marians KJ (2005). "Unwinding of the Nascent Lagging Strand by Rep and PriA Enables the Direct Restart of Stalled Replication Forks." J Biol Chem 280(40);34143-51. PMID: 16079128

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

Hiasa94: Hiasa H, Marians KJ (1994). "Primase couples leading- and lagging-strand DNA synthesis from oriC." J Biol Chem 269(8);6058-63. PMID: 8119951

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

Huang06c: Huang CY, Hsu CH, Sun YJ, Wu HN, Hsiao CD (2006). "Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA-binding mode." Nucleic Acids Res 34(14);3878-86. PMID: 16899446

Jezewska00: Jezewska MJ, Bujalowski W (2000). "Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA." Biochemistry 39(34);10454-67. PMID: 10956036

Jezewska00a: Jezewska MJ, Rajendran S, Bujalowski W (2000). "Escherichia coli replicative helicase PriA protein-single-stranded DNA complex. Stoichiometries, free energy of binding, and cooperativities." J Biol Chem 275(36);27865-73. PMID: 10875934

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

Johnson00a: 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

Jones01: Jones JM, Nakai H (2001). "Escherichia coli PriA helicase: fork binding orients the helicase to unwind the lagging strand side of arrested replication forks." J Mol Biol 312(5);935-47. PMID: 11580240

Jones99a: 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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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

Keck00: Keck JL, Roche DD, Lynch AS, Berger JM (2000). "Structure of the RNA polymerase domain of E. coli primase." Science 287(5462);2482-6. PMID: 10741967

Khopde02: Khopde S, Biswas EE, Biswas SB (2002). "Affinity and sequence specificity of DNA binding and site selection for primer synthesis by Escherichia coli primase." Biochemistry 41(50);14820-30. PMID: 12475230

Kogoma96: Kogoma T, Cadwell GW, Barnard KG, Asai T (1996). "The DNA replication priming protein, PriA, is required for homologous recombination and double-strand break repair." J Bacteriol 178(5);1258-64. PMID: 8631700

Konigsberg83: Konigsberg W, Godson GN (1983). "Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli." Proc Natl Acad Sci U S A 80(3);687-91. PMID: 6338495

Kozlov10: Kozlov AG, Jezewska MJ, Bujalowski W, Lohman TM (2010). "Binding specificity of Escherichia coli single-stranded DNA binding protein for the chi subunit of DNA pol III holoenzyme and PriA helicase." Biochemistry 49(17);3555-66. PMID: 20329707

Kruklitis94: Kruklitis R, Nakai H (1994). "Participation of the bacteriophage Mu A protein and host factors in the initiation of Mu DNA synthesis in vitro." J Biol Chem 269(23);16469-77. PMID: 8206956

Lark78: Lark CA, Riazi J, Lark KG (1978). "dnaT, dominant conditional-lethal mutation affecting DNA replication in Escherichia coli." J Bacteriol 136(3);1008-17. PMID: 363684

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

Lee87a: Lee MS, Marians KJ (1987). "Escherichia coli replication factor Y, a component of the primosome, can act as a DNA helicase." Proc Natl Acad Sci U S A 84(23);8345-9. PMID: 2825188

Lee89a: 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

Lee90: Lee EH, Masai H, Allen GC, Kornberg A (1990). "The priA gene encoding the primosomal replicative n' protein of Escherichia coli." Proc Natl Acad Sci U S A 1990;87(12);4620-4. PMID: 2162050

Lee90a: Lee MS, Marians KJ (1990). "Differential ATP requirements distinguish the DNA translocation and DNA unwinding activities of the Escherichia coli PRI A protein." J Biol Chem 265(28);17078-83. PMID: 2170365

Lee91a: Lee EH, Kornberg A (1991). "Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication n' protein." Proc Natl Acad Sci U S A 88(8);3029-32. PMID: 1826559

Lee92d: Lee EH, Kornberg A (1992). "Features of replication fork blockage by the Escherichia coli terminus-binding protein." J Biol Chem 267(13);8778-84. PMID: 1533620

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

Lilien82: Lilien C (1982). "Escherichia coli dnaG gene product is required for a normal rate of phage T4 DNA synthesis." Virology 123(2);443-7. PMID: 6758324

Liu04e: Liu JH, Chang TW, Huang CY, Chen SU, Wu HN, Chang MC, Hsiao CD (2004). "Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli." J Biol Chem 279(48);50465-71. PMID: 15383524

Liu96b: Liu J, Nurse P, Marians KJ (1996). "The ordered assembly of the phiX174-type primosome. III. PriB facilitates complex formation between PriA and DnaT." J Biol Chem 271(26);15656-61. PMID: 8663106

Liu99c: Liu J, Xu L, Sandler SJ, Marians KJ (1999). "Replication fork assembly at recombination intermediates is required for bacterial growth." Proc Natl Acad Sci U S A 96(7);3552-5. PMID: 10097074

Liu99d: Liu J, Marians KJ (1999). "PriA-directed assembly of a primosome on D loop DNA." J Biol Chem 274(35);25033-41. PMID: 10455182

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

Lopper04: Lopper M, Holton JM, Keck JL (2004). "Crystal structure of PriB, a component of the Escherichia coli replication restart primosome." Structure (Camb) 12(11);1967-75. PMID: 15530361

Lopper07: Lopper M, Boonsombat R, Sandler SJ, Keck JL (2007). "A hand-off mechanism for primosome assembly in replication restart." Mol Cell 26(6);781-93. PMID: 17588514

Loscha04: Loscha K, Oakley AJ, Bancia B, Schaeffer PM, Prosselkov P, Otting G, Wilce MC, Dixon NE (2004). "Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase." Protein Expr Purif 33(2);304-10. PMID: 14711519

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

Low82: Low RL, Shlomai J, Kornberg A (1982). "Protein n, a primosomal DNA replication protein of Escherichia coli. Purification and characterization." J Biol Chem 257(11);6242-50. PMID: 6281262

Lu96a: 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

Masai86: Masai H, Bond MW, Arai K (1986). "Cloning of the Escherichia coli gene for primosomal protein i: the relationship to dnaT, essential for chromosomal DNA replication." Proc Natl Acad Sci U S A 83(5);1256-60. PMID: 3006041

Masai88: Masai H, Arai K (1988). "Initiation of lagging-strand synthesis for pBR322 plasmid DNA replication in vitro is dependent on primosomal protein i encoded by dnaT." J Biol Chem 263(29);15016-23. PMID: 2844795

Masai88a: Masai H, Arai K (1988). "Operon structure of dnaT and dnaC genes essential for normal and stable DNA replication of Escherichia coli chromosome." J Biol Chem 1988;263(29);15083-93. PMID: 2844800

Masai89: Masai H, Arai K (1989). "Escherichia coli dnaT gene function is required for pBR322 plasmid replication but not for R1 plasmid replication." J Bacteriol 171(6);2975-80. PMID: 2656633

Masai89a: Masai H, Arai K (1989). "Leading strand synthesis of R1 plasmid replication in vitro is primed by primase alone at a specific site downstream of oriR." J Biol Chem 264(14);8082-90. PMID: 2542261

Masai90: Masai H, Nomura N, Kubota Y, Arai K (1990). "Roles of phi X174 type primosome- and G4 type primase-dependent primings in initiation of lagging and leading strand syntheses of DNA replication." J Biol Chem 265(25);15124-33. PMID: 2144283

Masai94: Masai H, Asai T, Kubota Y, Arai K, Kogoma T (1994). "Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication." EMBO J 13(22);5338-45. PMID: 7525276

McGlynn97: McGlynn P, Al-Deib AA, Liu J, Marians KJ, Lloyd RG (1997). "The DNA replication protein PriA and the recombination protein RecG bind D-loops." J Mol Biol 270(2);212-21. PMID: 9236123

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

Meddows04: Meddows TR, Savory AP, Lloyd RG (2004). "RecG helicase promotes DNA double-strand break repair." Mol Microbiol 52(1);119-32. PMID: 15049815

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

Mizukoshi03: Mizukoshi T, Tanaka T, Arai K, Kohda D, Masai H (2003). "A critical role of the 3' terminus of nascent DNA chains in recognition of stalled replication forks." J Biol Chem 278(43);42234-9. PMID: 12917421

Mok87: Mok M, Marians KJ (1987). "The Escherichia coli preprimosome and DNA B helicase can form replication forks that move at the same rate." J Biol Chem 262(34);16644-54. PMID: 2824502

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

Mustaev95: Mustaev AA, Godson GN (1995). "Studies of the functional topography of the catalytic center of Escherichia coli primase." J Biol Chem 270(26);15711-8. PMID: 7541046

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. I. Isolation and identification of intermediate protein-DNA complexes." J Biol Chem 271(26);15642-8. PMID: 8663104

Ng96a: 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

Nurse90: Nurse P, DiGate RJ, Zavitz KH, Marians KJ (1990). "Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y." Proc Natl Acad Sci U S A 87(12);4615-9. PMID: 2162049

Nurse91: Nurse P, Zavitz KH, Marians KJ (1991). "Inactivation of the Escherichia coli priA DNA replication protein induces the SOS response." J Bacteriol 173(21);6686-93. PMID: 1938875

Oakley05: Oakley AJ, Loscha KV, Schaeffer PM, Liepinsh E, Pintacuda G, Wilce MC, Otting G, Dixon NE (2005). "Crystal and solution structures of the helicase-binding domain of Escherichia coli primase." J Biol Chem 280(12);11495-504. PMID: 15649896

Ortega86: Ortega S, Lanka E, Diaz R (1986). "The involvement of host replication proteins and of specific origin sequences in the in vitro replication of miniplasmid R1 DNA." Nucleic Acids Res 14(12);4865-79. PMID: 3523437

Ouzounis91: Ouzounis CA, Blencowe BJ (1991). "Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD-box' family." Nucleic Acids Res 19(24);6953. PMID: 1662369

Pinkney88: Pinkney M, Diaz R, Lanka E, Thomas CM (1988). "Replication of mini RK2 plasmid in extracts of Escherichia coli requires plasmid-encoded protein TrfA and host-encoded proteins DnaA, B, G DNA gyrase and DNA polymerase III." J Mol Biol 203(4);927-38. PMID: 2850370

Podobnik00: Podobnik M, McInerney P, O'Donnell M, Kuriyan J (2000). "A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases." J Mol Biol 300(2);353-62. PMID: 10873470

Ponomarev03: Ponomarev VA, Makarova KS, Aravind L, Koonin EV (2003). "Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb." J Mol Microbiol Biotechnol 5(4);225-9. PMID: 12867746

Powers99: Powers L, Griep MA (1999). "Escherichia coli primase zinc is sensitive to substrate and cofactor binding." Biochemistry 38(23);7413-20. PMID: 10360938

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

Rangarajan02: Rangarajan S, Woodgate R, Goodman MF (2002). "Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins." Mol Microbiol 43(3);617-28. PMID: 11929519

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

Rowen78: Rowen L, Kornberg A (1978). "Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains." J Biol Chem 253(3);758-64. PMID: 340457

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

Sandler00: Sandler SJ (2000). "Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12." Genetics 155(2);487-97. PMID: 10835375

Sandler05: Sandler SJ (2005). "Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12." Genetics 169(4);1799-806. PMID: 15716497

Sandler99: Sandler SJ, Marians KJ, Zavitz KH, Coutu J, Parent MA, Clark AJ (1999). "dnaC mutations suppress defects in DNA replication- and recombination-associated functions in priB and priC double mutants in Escherichia coli K-12." Mol Microbiol 34(1);91-101. PMID: 10540288

Sasaki06: Sasaki K, Ose T, Tanaka T, Mizukoshi T, Ishigaki T, Maenaka K, Masai H, Kohda D (2006). "Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli." Biochim Biophys Acta 1764(1);157-60. PMID: 16226927

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

Scherzinger91: Scherzinger E, Haring V, Lurz R, Otto S (1991). "Plasmid RSF1010 DNA replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins." Nucleic Acids Res 19(6);1203-11. PMID: 1851552

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

Shioi05: Shioi S, Ose T, Maenaka K, Shiroishi M, Abe Y, Kohda D, Katayama T, Ueda T (2005). "Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site." Biochem Biophys Res Commun 326(4);766-76. PMID: 15607735

Sims80: Sims J, Benz EW (1980). "Initiation of DNA replication by the Escherichia coli dnaG protein: evidence that tertiary structure is involved." Proc Natl Acad Sci U S A 77(2);900-4. PMID: 6244591

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

Soeller82: Soeller WC, Marians KJ (1982). "Deletion mutants defining the Escherichia coli replication factor Y effector site sequences in pBR322 DNA." Proc Natl Acad Sci U S A 79(23);7253-7. PMID: 6130524

Stamford92: Stamford NP, Lilley PE, Dixon NE (1992). "Enriched sources of Escherichia coli replication proteins. The dnaG primase is a zinc metalloprotein." Biochim Biophys Acta 1132(1);17-25. PMID: 1511009

Stayton83a: Stayton MM, Kornberg A (1983). "Complexes of Escherichia coli primase with the replication origin of G4 phage DNA." J Biol Chem 258(21);13205-12. PMID: 6355106

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

Sun98: Sun W, Godson GN (1998). "Structure of the Escherichia coli primase/single-strand DNA-binding protein/phage G4oric complex required for primer RNA synthesis." J Mol Biol 276(4);689-703. PMID: 9500915

Sun98a: Sun W, Godson GN (1998). "Synthesis of polyribonucleotide chains from the 3'-hydroxyl terminus of oligodeoxynucleotides by Escherichia coli primase." J Biol Chem 273(26);16358-65. PMID: 9632699

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

Swart93: Swart JR, Griep MA (1993). "Primase from Escherichia coli primes single-stranded templates in the absence of single-stranded DNA-binding protein or other auxiliary proteins. Template sequence requirements based on the bacteriophage G4 complementary strand origin and Okazaki fragment initiation sites." J Biol Chem 268(17);12970-6. PMID: 8509429

Swart95: Swart JR, Griep MA (1995). "Primer synthesis kinetics by Escherichia coli primase on single-stranded DNA templates." Biochemistry 34(49);16097-106. PMID: 8519767

Tanaka02a: Tanaka T, Mizukoshi T, Taniyama C, Kohda D, Arai K, Masai H (2002). "DNA binding of PriA protein requires cooperation of the N-terminal D-loop/arrested-fork binding and C-terminal helicase domains." J Biol Chem 277(41);38062-71. PMID: 12151393

Tanaka03: Tanaka T, Taniyama C, Arai K, Masai H (2003). "ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination-dependent DNA replication." Genes Cells 8(3);251-61. PMID: 12622722

Tanaka94: Tanaka K, Rogi T, Hiasa H, Miao DM, Honda Y, Nomura N, Sakai H, Komano T (1994). "Comparative analysis of functional and structural features in the primase-dependent priming signals, G sites, from phages and plasmids." J Bacteriol 176(12);3606-13. PMID: 8206839

Tougu94: Tougu K, Peng H, Marians KJ (1994). "Identification of a domain of Escherichia coli primase required for functional interaction with the DnaB helicase at the replication fork." J Biol Chem 269(6);4675-82. PMID: 8308039

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Urlacher95: Urlacher TM, Griep MA (1995). "Magnesium acetate induces a conformational change in Escherichia coli primase." Biochemistry 34(51);16708-14. PMID: 8527445

vanderEnde85: van der Ende A, Baker TA, Ogawa T, Kornberg A (1985). "Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: primase as the sole priming enzyme." Proc Natl Acad Sci U S A 82(12);3954-8. PMID: 2408271

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

Wickner75a: Wickner S, Hurwitz J (1975). "Association of phiX174 DNA-dependent ATPase activity with an Escherichia coli protein, replication factor Y, required for in vitro synthesis of phiX174 DNA." Proc Natl Acad Sci U S A 72(9);3342-6. PMID: 127175

Wu92c: 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

Wu92d: Wu CA, Zechner EL, Reems JA, McHenry CS, Marians KJ (1992). "Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. V. Primase action regulates the cycle of Okazaki fragment synthesis." J Biol Chem 267(6);4074-83. PMID: 1740453

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

Yajnik93: Yajnik V, Godson GN (1993). "Selective decay of Escherichia coli dnaG messenger RNA is initiated by RNase E." J Biol Chem 1993;268(18);13253-60. PMID: 7685758

Yamamoto09: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369

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

Yang02c: 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

Yang04: Yang H, Wolff E, Kim M, Diep A, Miller JH (2004). "Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach." Mol Microbiol 53(1);283-95. PMID: 15225322

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

Yuzhakov99: Yuzhakov A, Kelman Z, O'Donnell M (1999). "Trading places on DNA--a three-point switch underlies primer handoff from primase to the replicative DNA polymerase." Cell 96(1);153-63. PMID: 9989506

Zavitz91: Zavitz KH, DiGate RJ, Marians KJ (1991). "The priB and priC replication proteins of Escherichia coli. Genes, DNA sequence, overexpression, and purification." J Biol Chem 266(21);13988-95. PMID: 1856227

Zavitz92: Zavitz KH, Marians KJ (1992). "ATPase-deficient mutants of the Escherichia coli DNA replication protein PriA are capable of catalyzing the assembly of active primosomes." J Biol Chem 267(10);6933-40. PMID: 1313026

Zechner92: Zechner EL, Wu CA, Marians KJ (1992). "Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size." J Biol Chem 267(6);4054-63. PMID: 1531480

Zechner92a: Zechner EL, Wu CA, Marians KJ (1992). "Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. II. Frequency of primer synthesis and efficiency of primer utilization control Okazaki fragment size." J Biol Chem 267(6);4045-53. PMID: 1740452

Zhang02g: Zhang Y, Yang F, Kao YC, Kurilla MG, Pompliano DL, Dicker IB (2002). "Homogenous assays for Escherichia coli DnaB-stimulated DnaG primase and DnaB helicase and their use in screening for chemical inhibitors." Anal Biochem 304(2);174-9. PMID: 12009693

Zipursky80: Zipursky SL, Marians KJ (1980). "Identification of two Escherichia coli factor Y effector sites near the origins of replication of the plasmids (ColE1 and pBR322." Proc Natl Acad Sci U S A 77(11);6521-5. PMID: 6109282

Zipursky81: Zipursky SL, Marians KJ (1981). "Escherichia coli factor Y sites of plasmid pBR322 can function as origins of DNA replication." Proc Natl Acad Sci U S A 78(10);6111-5. PMID: 6273849


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