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Escherichia coli K-12 substr. MG1655 Polypeptide: chromosome replication; initiation and chain elongation



Gene: dnaC Accession Numbers: EG10237 (EcoCyc), b4361, ECK4351

Synonyms: dnaD

Regulation Summary Diagram: ?

Summary:
DnaC is an accessory protein that loads the DnaB replicative helicase onto duplex DNA to initiate replication and onto single-stranded DNA to assist in primer formation by primase [Wickner75, Marszalek94, Wahle89, Wahle89a]. As a consequence, DnaC is required for replication initiation, primer synthesis and restarting at stalled replication forks [Kaguni85, NussleinCrystal82]. Following binding of the replication initiator protein DnaA at the origin of replication oriC, DnaC loads DnaB onto the same site to yield an asymmetric prepriming complex consisting of DnaA and DnaB [Kung78, Funnell87]. Following loading by DnaC, DnaB unwinds DNA in both directions from oriC [Baker87].

The interaction between DnaC and DnaB is complex and has consequences for DnaB activation and subsequent function. DnaC and DnaB bind in an ATP-dependent manner [Wickner75]. With DnaB and ATP engaged, DnaC is then able to bind single-stranded DNA (ssDNA) [Learn97]. Following binding, DnaC hydrolyzes its ATP, resulting in a fifty-fold drop in its affinity for ssDNA and thus release from both the DNA and DnaB [Davey02, Biswas04]. Even though ATP hydrolysis has no direct effect on binding of DnaC to DnaB, when it is blocked, DnaB helicase activity is severely curtailed due to the inhibitory effect of DnaC that remains bound to the DNA [Biswas87, Galletto03, Wahle89a, Biswas86]. DnaB helicase function has been shown both in vitro and in vivo to depend on the relative quantity of DnaB and DnaC, being inversely proportional to the amount of excess DnaC present [Allen91, Skarstad95]. This may explain the lethality of DnaC overexpression [Ludlam01].

The temporary DnaC-DnaB complex consists of six DnaC monomers bound to the hexameric DnaB helicase [Lanka83, Kobori82]. Thus, even though isolated DnaC is a monomer, it still experiences cooperativity in response to ATP binding when the DnaB hexamer is present [Galletto04]. Based on cryo-EM studies of the DnaC-DnaB complex, the DnaC monomers arrange as three dimers that bind to the three-fold symmetric face of the DnaB hexamer, maintaining that symmetry after binding [San98, Donate00, Barcena01].

The amino-terminal domain of DnaC is required for binding DnaB but not for binding ATP [Ludlam01]. Based on similarity studies, DnaC does contain an ATP-binding motif that is similar to that found in DnaA [Koonin92]. DnaC binds one ATP per DnaC monomer; this binding has been examined in detail [Galletto00, Galletto02, Galletto05]. DnaC undergoes a conformational change required for ATP binding that has also been the subject of detailed analysis [Galletto02a]. Release of ATP from the binding site requires the presence of divalent magnesium ion [Galletto04]. Mutations in the carboxy-terminal domain of DnaC suppress mutations in priA [Sandler96].

Replication mutants including dnaC have lower levels of unsaturation in their fatty acids [Suzuki98]. In addition, conditional dnaC mutants have problems completing chromosomal replication, especially in rep-mutated strains. This suggests a possible role for DnaC in replication restart following double-strand breaks [MaisnierPatin01]. dnaC mutation also partially suppresses priBC double mutants [Sandler99].

Citations: [Davey03, Schaeffer05, Kobori82a]

Gene Citations: [Masai88]

Locations: cytosol

Map Position: [4,598,261 <- 4,598,998] (99.11 centisomes)
Length: 738 bp / 245 aa

Molecular Weight of Polypeptide: 27.935 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014304 , CGSC:849 , DIP:DIP-9457N , EchoBASE:EB0233 , EcoGene:EG10237 , EcoliWiki:b4361 , Mint:MINT-1276712 , ModBase:P0AEF0 , OU-Microarray:b4361 , PortEco:dnaC , PR:PRO_000022461 , Pride:P0AEF0 , Protein Model Portal:P0AEF0 , RefSeq:NP_418781 , RegulonDB:EG10237 , SMR:P0AEF0 , String:511145.b4361 , UniProt:P0AEF0

Relationship Links: InterPro:IN-FAMILY:IPR002611 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR027417 , InterPro:IN-FAMILY:IPR028350 , Pfam:IN-FAMILY:PF01695 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 281 (4 members)

GO Terms:

Biological Process: GO:0006271 - DNA strand elongation involved in DNA replication Inferred from experiment [NussleinCrystal82]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, AriasPalomo13, Ng96, MakowskaGrzyska10, Butland05]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes cell division
information transfer DNA related DNA replication

Essentiality data for dnaC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 6
[Nakayama87, Masai86, UniProt10]
Alternate sequence: D → A; UniProt: (in Ref. 1 and 6);
Amino-Acid-Site 69
[UniProt10]
UniProt: Probably involved in the interaction with the dnaB protein; Sequence Annotation Type: site;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4361 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10237; confirmed by SwissProt match.


References

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

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

Biswas04: Biswas SB, Flowers S, Biswas-Fiss EE (2004). "Quantitative analysis of nucleotide modulation of DNA binding by DnaC protein of Escherichia coli." Biochem J 379(Pt 3);553-62. PMID: 14715083

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

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

Davey02: Davey MJ, Fang L, McInerney P, Georgescu RE, O'Donnell M (2002). "The DnaC helicase loader is a dual ATP/ADP switch protein." EMBO J 21(12);3148-59. PMID: 12065427

Davey03: Davey MJ, O'Donnell M (2003). "Replicative helicase loaders: ring breakers and ring makers." Curr Biol 13(15);R594-6. PMID: 12906810

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

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

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

Galletto00: Galletto R, Rajendran S, Bujalowski W (2000). "Interactions of nucleotide cofactors with the Escherichia coli replication factor DnaC protein." Biochemistry 39(42);12959-69. PMID: 11041861

Galletto02: Galletto R, Bujalowski W (2002). "Kinetics of the E. coli replication factor DnaC protein-nucleotide interactions. II. Fluorescence anisotropy and transient, dynamic quenching stopped-flow studies of the reaction intermediates." Biochemistry 41(28);8921-34. PMID: 12102634

Galletto02a: Galletto R, Bujalowski W (2002). "The E. coli replication factor DnaC protein exists in two conformations with different nucleotide binding capabilities. I. Determination of the binding mechanism using ATP and ADP fluorescent analogues." Biochemistry 41(28);8907-20. PMID: 12102633

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, Maillard R, Jezewska MJ, Bujalowski W (2004). "Global conformation of the Escherichia coli replication factor DnaC protein in absence and presence of nucleotide cofactors." Biochemistry 43(34);10988-1001. PMID: 15323558

Galletto05: Galletto R, Jezewska MJ, Maillard R, Bujalowski W (2005). "The nucleotide-binding site of the Escherichia coli DnaC protein: molecular topography of DnaC protein-nucleotide cofactor complexes." Cell Biochem Biophys 43(3);331-53. PMID: 16244362

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

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

Kobori82: Kobori JA, Kornberg A (1982). "The Escherichia coli dnaC gene product. III. Properties of the dnaB-dnaC protein complex." J Biol Chem 257(22);13770-5. PMID: 6292205

Kobori82a: Kobori JA, Kornberg A (1982). "The Escherichia coli dnaC gene product. II. Purification, physical properties, and role in replication." J Biol Chem 257(22);13763-9. PMID: 6292204

Koonin92: Koonin EV (1992). "DnaC protein contains a modified ATP-binding motif and belongs to a novel family of ATPases including also DnaA." Nucleic Acids Res 20(8);1997. PMID: 1533715

Kung78: Kung FC, Glaser DA (1978). "dnaA acts before dnaC in the initiation of DNA replication." J Bacteriol 133(2);755-62. PMID: 627535

Lanka83: Lanka E, Schuster H (1983). "The dnaC protein of Escherichia coli. Purification, physical properties and interaction with dnaB protein." Nucleic Acids Res 11(4);987-97. PMID: 6298736

Learn97: Learn BA, Um SJ, Huang L, McMacken R (1997). "Cryptic single-stranded-DNA binding activities of the phage lambda P and Escherichia coli DnaC replication initiation proteins facilitate the transfer of E. coli DnaB helicase onto DNA." Proc Natl Acad Sci U S A 94(4);1154-9. PMID: 9037022

Ludlam01: Ludlam AV, McNatt MW, Carr KM, Kaguni JM (2001). "Essential amino acids of Escherichia coli DnaC protein in an N-terminal domain interact with DnaB helicase." J Biol Chem 276(29);27345-53. PMID: 11333269

MaisnierPatin01: Maisnier-Patin S, Nordstrom K, Dasgupta S (2001). "Replication arrests during a single round of replication of the Escherichia coli chromosome in the absence of DnaC activity." Mol Microbiol 42(5);1371-82. PMID: 11886566

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

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). "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

Nakayama87: Nakayama N, Bond MW, Miyajima A, Kobori J, Arai K (1987). "Structure of Escherichia coli dnaC. Identification of a cysteine residue possibly involved in association with dnaB protein." J Biol Chem 262(22);10475-80. PMID: 3301836

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

NussleinCrystal82: Nusslein-Crystalla V, Niedenhof I, Rein R (1982). "dnaC-dependent reconstitution of replication forks in Escherichia coli lysates." J Bacteriol 150(1);286-92. PMID: 6277866

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

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

Sandler96: Sandler SJ, Samra HS, Clark AJ (1996). "Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC." Genetics 143(1);5-13. PMID: 8722757

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

Schaeffer05: Schaeffer PM, Headlam MJ, Dixon NE (2005). "Protein--protein interactions in the eubacterial replisome." IUBMB Life 57(1);5-12. PMID: 16036556

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

Suzuki98: Suzuki E, Kondo T, Makise M, Mima S, Sakamoto K, Tsuchiya T, Mizushima T (1998). "Alteration in levels of unsaturated fatty acids in mutants of Escherichia coli defective in DNA replication." Biol Pharm Bull 21(7);657-61. PMID: 9703244

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: 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

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

Other References Related to Gene Regulation

Olson82: Olson ER, Flamm EL, Friedman DI (1982). "Analysis of nutR: a region of phage lambda required for antitermination of transcription." Cell 31(1);61-70. PMID: 6218883


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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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