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Escherichia coli K-12 substr. MG1655 Polypeptide: branch migration of Holliday structures; repair



Gene: ruvA Accession Numbers: RUVA (EcoCyc), b1861, ECK1862

Regulation Summary Diagram: ?

Component of: resolvasome (extended summary available)

Summary:
RuvA is a structure specific DNA binding protein which has high affinity for Holliday junctions. Together with RuvA it mediates branch migration of Holliday junctions.

Gene Citations: [Benson88, Iwasaki89, Shinagawa88]

Locations: cytosol

Map Position: [1,943,389 <- 1,944,000] (41.89 centisomes)
Length: 612 bp / 203 aa

Molecular Weight of Polypeptide: 22.086 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006206 , CGSC:17923 , DIP:DIP-48064N , EchoBASE:EB0916 , EcoGene:EG10923 , EcoliWiki:b1861 , Mint:MINT-1321234 , ModBase:P0A809 , OU-Microarray:b1861 , PortEco:ruvA , PR:PRO_000023900 , Pride:P0A809 , Protein Model Portal:P0A809 , RefSeq:NP_416375 , RegulonDB:RUVA , SMR:P0A809 , String:511145.b1861 , UniProt:P0A809

Relationship Links: InterPro:IN-FAMILY:IPR000085 , InterPro:IN-FAMILY:IPR003583 , InterPro:IN-FAMILY:IPR010994 , InterPro:IN-FAMILY:IPR011114 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR013849 , PDB:Structure:1BDX , PDB:Structure:1C7Y , PDB:Structure:1CUK , PDB:Structure:1D8L , PDB:Structure:1HJP , Pfam:IN-FAMILY:PF01330 , Pfam:IN-FAMILY:PF07499 , Smart:IN-FAMILY:SM00278

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000725 - recombinational repair Inferred from experiment [Lloyd84]
GO:0009432 - SOS response Inferred from experiment Inferred by computational analysis [UniProtGOA11, Shinagawa88, Benson88]
GO:0032508 - DNA duplex unwinding Inferred by computational analysis Inferred from experiment [Tsaneva92, GOA01a]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0009378 - four-way junction helicase activity Inferred from experiment Inferred by computational analysis [GOA01a, Tsaneva92]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0003678 - DNA helicase activity Inferred by computational analysis [GOA01a]
GO:0004386 - helicase activity Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0009379 - Holliday junction helicase complex Inferred from experiment Inferred by computational analysis [GOA01a, Tsaneva92]
GO:0048476 - Holliday junction resolvase complex Inferred from experiment [Eggleston97]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes SOS response
information transfer DNA related DNA recombination
information transfer DNA related DNA repair

Essentiality data for ruvA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
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: resolvasome

Synonyms: RuvABC

Subunit composition of resolvasome = [RuvC]2[RuvB]12[RuvA]4
         Holliday junction nuclease; resolution of structures; repair = RuvC (summary available)
         branch migration of Holliday structures; repair helicase = RuvB (summary available)
         branch migration of Holliday structures; repair = RuvA (summary available)

Summary:
The E. coli 'resolvasome' is an enzymatic complex of 3 proteins - RuvA, RuvB and RuvC - which function together to resolve Holliday junctions formed during the recombinational repair of damaged double strand DNA. The RuvAB complex also plays an important role in the rescue of blocked DNA replication forks via a process known as replication fork reversal [Seigneur98, Baharoglu06].

Overexpressed purified RuvA is tetrameric in solution [Tsaneva92a] and binds both single and double strand DNA [Shiba91]. Purified RuvB has a low ATPase activity which is enhanced by RuvA in the presence of DNA [Shiba91, Iwasaki89a]. In the presence of ATP, RuvA and RuvB promote branch migration and the dissociation of synthetic Holliday structures [Parsons92] and recombination intermediates made by RecA [Tsaneva92, Iwasaki92]. RuvC interacts with synthetic Holliday junctions and RecA mediated intermediates in vitro and promotes their resolution by introducing nicks into two homologous strands of the same polarity [Iwasaki91, Connolly91, Shah94a, Dunderdale94]. RuvC resolves recombination intermediates at specific sites with the consensus sequence 5'(A/T)TT(G/C)3' [Shah94a, Shah97]. RuvC binds its DNA substrate as a dimer [Iwasaki91].

RuvA and RuvB interact in solution as well as at Holliday junctions [Parsons93]. RuvA and RuvB form a complex comprised of a tetramer of RuvA and two hexamers of RuvB [Stasiak94, Rafferty96, Yu97]. RuvB interacts directly with RuvC in an in vitro reconstituted system for the formation and resolution of Holliday junctions [Eggleston97].

Mutations in ruvA, ruvB or ruvC increase sensitivity to UV light, ionizing radiation and mitomycin C [Iwasaki89, Lloyd84, Otsuji74]. ruvA and ruvB were found to be organized into an SOS-inducible operon but ruvC belongs to an adjacent, non-inducible operon [Benson88, Shinagawa88, Sharples90].

Reviews: [West92, Kuzminov93, Shinagawa95, Shinagawa96, West96, West97b, Michel07]

Citations: [Osman09, Le08, Bradley11]

GO Terms:

Biological Process: GO:0000725 - recombinational repair Inferred from experiment [Lloyd84]
GO:0071932 - replication fork reversal Inferred from experiment [Seigneur98]
Cellular Component: GO:0048476 - Holliday junction resolvase complex Inferred from experiment [Eggleston97]

Credits:
Last-Curated ? 30-Jun-2011 by Mackie A , Macquarie University


Enzymatic reaction of: resolvasome

EC Number: 3.1.22.4

DNA combined with exogenous DNA to form a recombinational junction + H2O <=> resolution of recombinational junction formation of two intact strands

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

pH(opt): 7 [BRENDA14, Takahagi94]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 166
[Benson88, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 1; CAA30119);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1861 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10923; confirmed by SwissProt match.


References

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

Baharoglu06: Baharoglu Z, Petranovic M, Flores MJ, Michel B (2006). "RuvAB is essential for replication forks reversal in certain replication mutants." EMBO J 25(3);596-604. PMID: 16424908

Benson88: Benson FE, Illing GT, Sharples GJ, Lloyd RG (1988). "Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes." Nucleic Acids Res 16(4);1541-9. PMID: 3279394

Bradley11: Bradley AS, Baharoglu Z, Niewiarowski A, Michel B, Tsaneva IR (2011). "Formation of a Stable RuvA Protein Double Tetramer Is Required for Efficient Branch Migration in Vitro and for Replication Fork Reversal in Vivo." J Biol Chem 286(25);22372-83. PMID: 21531731

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Connolly91: Connolly B, Parsons CA, Benson FE, Dunderdale HJ, Sharples GJ, Lloyd RG, West SC (1991). "Resolution of Holliday junctions in vitro requires the Escherichia coli ruvC gene product." Proc Natl Acad Sci U S A 88(14);6063-7. PMID: 1829835

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

Dunderdale94: Dunderdale HJ, Sharples GJ, Lloyd RG, West SC (1994). "Cloning, overexpression, purification, and characterization of the Escherichia coli RuvC Holliday junction resolvase." J Biol Chem 269(7);5187-94. PMID: 8106500

Eggleston97: Eggleston AK, Mitchell AH, West SC (1997). "In vitro reconstitution of the late steps of genetic recombination in E. coli." Cell 89(4);607-17. PMID: 9160752

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Iwasaki89: Iwasaki H, Shiba T, Nakata A, Shinagawa H (1989). "Involvement in DNA repair of the ruvA gene of Escherichia coli." Mol Gen Genet 1989;219(1-2);328-31. PMID: 2693946

Iwasaki89a: Iwasaki H, Shiba T, Makino K, Nakata A, Shinagawa H (1989). "Overproduction, purification, and ATPase activity of the Escherichia coli RuvB protein involved in DNA repair." J Bacteriol 171(10);5276-80. PMID: 2529252

Iwasaki91: Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H (1991). "Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure." EMBO J 10(13);4381-9. PMID: 1661673

Iwasaki92: Iwasaki H, Takahagi M, Nakata A, Shinagawa H (1992). "Escherichia coli RuvA and RuvB proteins specifically interact with Holliday junctions and promote branch migration." Genes Dev 6(11);2214-20. PMID: 1427081

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

Kuzminov93: Kuzminov A (1993). "RuvA, RuvB and RuvC proteins: cleaning-up after recombinational repairs in E. coli." Bioessays 15(5);355-8. PMID: 8393667

Le08: Le Masson M, Baharoglu Z, Michel B (2008). "ruvA and ruvB mutants specifically impaired for replication fork reversal." Mol Microbiol 70(2);537-48. PMID: 18942176

Lloyd84: Lloyd RG, Benson FE, Shurvinton CE (1984). "Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12." Mol Gen Genet 194(1-2);303-9. PMID: 6374379

Michel07: Michel B, Boubakri H, Baharoglu Z, LeMasson M, Lestini R (2007). "Recombination proteins and rescue of arrested replication forks." DNA Repair (Amst) 6(7);967-80. PMID: 17395553

Osman09: Osman F, Gaskell L, Whitby MC (2009). "Efficient second strand cleavage during Holliday junction resolution by RuvC requires both increased junction flexibility and an exposed 5' phosphate." PLoS One 4(4);e5347. PMID: 19399178

Otsuji74: Otsuji N, Iyehara H, Hideshima Y (1974). "Isolation and characterization of an Escherichia coli ruv mutant which forms nonseptate filaments after low doses of ultraviolet light irradiation." J Bacteriol 117(2);337-44. PMID: 4590461

Parsons92: Parsons CA, Tsaneva I, Lloyd RG, West SC (1992). "Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions." Proc Natl Acad Sci U S A 89(12);5452-6. PMID: 1608954

Parsons93: Parsons CA, West SC (1993). "Formation of a RuvAB-Holliday junction complex in vitro." J Mol Biol 232(2);397-405. PMID: 8393934

Rafferty96: Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG, Rice DW (1996). "Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction." Science 274(5286);415-21. PMID: 8832889

Seigneur98: Seigneur M, Bidnenko V, Ehrlich SD, Michel B (1998). "RuvAB acts at arrested replication forks." Cell 95(3);419-30. PMID: 9814711

Shah94: Shah R, Bennett RJ, West SC (1994). "Activation of RuvC Holliday junction resolvase in vitro." Nucleic Acids Res 22(13);2490-7. PMID: 8041610

Shah94a: Shah R, Bennett RJ, West SC (1994). "Genetic recombination in E. coli: RuvC protein cleaves Holliday junctions at resolution hotspots in vitro." Cell 79(5);853-64. PMID: 8001122

Shah97: Shah R, Cosstick R, West SC (1997). "The RuvC protein dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts." EMBO J 16(6);1464-72. PMID: 9135161

Sharples90: Sharples GJ, Benson FE, Illing GT, Lloyd RG (1990). "Molecular and functional analysis of the ruv region of Escherichia coli K-12 reveals three genes involved in DNA repair and recombination." Mol Gen Genet 221(2);219-26. PMID: 2164626

Shiba91: Shiba T, Iwasaki H, Nakata A, Shinagawa H (1991). "SOS-inducible DNA repair proteins, RuvA and RuvB, of Escherichia coli: functional interactions between RuvA and RuvB for ATP hydrolysis and renaturation of the cruciform structure in supercoiled DNA." Proc Natl Acad Sci U S A 88(19);8445-9. PMID: 1833759

Shinagawa88: Shinagawa H, Makino K, Amemura M, Kimura S, Iwasaki H, Nakata A (1988). "Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination." J Bacteriol 1988;170(9);4322-9. PMID: 2842314

Shinagawa95: Shinagawa H, Iwasaki H (1995). "Molecular mechanisms of Holliday junction processing in Escherichia coli." Adv Biophys 31;49-65. PMID: 7625278

Shinagawa96: Shinagawa H, Iwasaki H (1996). "Processing the holliday junction in homologous recombination." Trends Biochem Sci 21(3);107-11. PMID: 8882584

Stasiak94: Stasiak A, Tsaneva IR, West SC, Benson CJ, Yu X, Egelman EH (1994). "The Escherichia coli RuvB branch migration protein forms double hexameric rings around DNA." Proc Natl Acad Sci U S A 91(16);7618-22. PMID: 8052630

Takahagi94: Takahagi M, Iwasaki H, Shinagawa H (1994). "Structural requirements of substrate DNA for binding to and cleavage by RuvC, a Holliday junction resolvase." J Biol Chem 269(21);15132-9. PMID: 8195150

Tsaneva92: Tsaneva IR, Muller B, West SC (1992). "ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli." Cell 69(7);1171-80. PMID: 1617728

Tsaneva92a: Tsaneva IR, Illing G, Lloyd RG, West SC (1992). "Purification and properties of the RuvA and RuvB proteins of Escherichia coli." Mol Gen Genet 235(1);1-10. PMID: 1435721

UniProt10a: 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."

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

West92: West SC, Connolly B (1992). "Biological roles of the Escherichia coli RuvA, RuvB and RuvC proteins revealed." Mol Microbiol 6(19);2755-9. PMID: 1435254

West96: West SC (1996). "The RuvABC proteins and Holliday junction processing in Escherichia coli." J Bacteriol 178(5);1237-41. PMID: 8631697

West97b: West SC (1997). "Processing of recombination intermediates by the RuvABC proteins." Annu Rev Genet 31;213-44. PMID: 9442895

Yu97: Yu X, West SC, Egelman EH (1997). "Structure and subunit composition of the RuvAB-Holliday junction complex." J Mol Biol 266(2);217-22. PMID: 9047358

Other References Related to Gene Regulation

Fernandez00: Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R (2000). "Identification of additional genes belonging to the LexA regulon in Escherichia coli." Mol Microbiol 35(6);1560-72. PMID: 10760155

Lewis94: Lewis LK, Harlow GR, Gregg-Jolly LA, Mount DW (1994). "Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli." J Mol Biol 241(4);507-23. PMID: 8057377


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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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