Escherichia coli K-12 substr. MG1655 Polypeptide: DNA recombination protein

Gene: radA Accession Numbers: EG11296 (EcoCyc), b4389, ECK4381

Synonyms: sms

Regulation Summary Diagram: ?

Regulation summary diagram for radA

RadA is involved in the processing of DNA recombination intermediates [Beam02].

A radA null mutant exhibits a modest defect in conjugational DNA recombination [Beam02]. radA mutants exhibit greater sensitivity to methylmethane sulfonate [Neuwald92, Song96, Beam02], phleomycin [Beam02], ciprofloxacin [Cooper15] and to UV irradiation than wild type [Song96]. Mutations in radA are synergistic with mutations in recG and ruvABC for recombination and tolerance to DNA damage which suggests RadA may function in the processing of DNA recombination intermediates [Beam02, Cooper15]. Mutations in radA are synergistic with mutations in DNA helicases (eg. lhr, dinG, priA, rep, uvrD, radD, yoaA) for sensitivity to the DNA damaging agents ciprofloxacin and azidothymidine [Cooper15].

RadA has a zinc finger motif (CX2CXnCX2C) located in the N-terminal region of the protein and an ATP/GTP-binding motif. RadA has similarity to Lon and RecA [Neuwald92].

radA and serB are cotranscribed [Neuwald92].

sms: sensitivity to methylmethane sulfonate
rad: radiation sensitivity

Citations: [Kruger97]

Locations: cytosol

Map Position: [4,623,935 -> 4,625,317] (99.66 centisomes, 359°)
Length: 1383 bp / 460 aa

Molecular Weight of Polypeptide: 49.472 kD (from nucleotide sequence), 55 kD (experimental)

Unification Links: ASAP:ABE-0014395 , CGSC:34653 , DIP:DIP-10635N , EchoBASE:EB1273 , EcoGene:EG11296 , EcoliWiki:b4389 , ModBase:P24554 , OU-Microarray:b4389 , PortEco:radA , PR:PRO_000023675 , Pride:P24554 , Protein Model Portal:P24554 , RefSeq:NP_418806 , RegulonDB:EG11296 , SMR:P24554 , String:511145.b4389 , UniProt:P24554

Relationship Links: InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR004504 , InterPro:IN-FAMILY:IPR014721 , InterPro:IN-FAMILY:IPR020568 , InterPro:IN-FAMILY:IPR020588 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR32472 , Prints:IN-FAMILY:PR01874 , Prosite:IN-FAMILY:PS50162 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 139 (3 members) , 445 (2 members)

GO Terms:

Biological Process: GO:0000725 - recombinational repair Inferred from experiment [Beam02]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0003684 - damaged DNA binding Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008094 - DNA-dependent ATPase activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA recombination
information transfer DNA related DNA repair

Essentiality data for radA 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]

Sequence Features

Protein sequence of DNA recombination protein with features indicated

Feature Class Location Citations Comment
Zn-Finger-Region 11 -> 28
[UniProt10, Neuwald92]
UniProt: C4-type; Non-Experimental Qualifier: potential;
Nucleotide-Phosphate-Binding-Region 102 -> 109
[UniProt10, Neuwald92]
UniProt: ATP; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G769/b4389 and EG11296/sms
10/20/97 Gene b4389 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11296; confirmed by SwissProt match.


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

Beam02: Beam CE, Saveson CJ, Lovett ST (2002). "Role for radA/sms in recombination intermediate processing in Escherichia coli." J Bacteriol 184(24);6836-44. PMID: 12446634

Cooper15: Cooper DL, Boyle DC, Lovett ST (2015). "Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions." Mol Microbiol 95(5);769-79. PMID: 25484163

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

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."

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

Kruger97: Kruger E, Msadek T, Ohlmeier S, Hecker M (1997). "The Bacillus subtilis clpC operon encodes DNA repair and competence proteins." Microbiology 143 ( Pt 4);1309-16. PMID: 9141693

Neuwald92: Neuwald AF, Berg DE, Stauffer GV (1992). "Mutational analysis of the Escherichia coli serB promoter region reveals transcriptional linkage to a downstream gene." Gene 1992;120(1);1-9. PMID: 1327967

Song96: Song Y, Sargentini NJ (1996). "Escherichia coli DNA repair genes radA and sms are the same gene." J Bacteriol 178(16);5045-8. PMID: 8759876

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Other References Related to Gene Regulation

Neuwald85: Neuwald AF, Stauffer GV (1985). "DNA sequence and characterization of the Escherichia coli serB gene." Nucleic Acids Res 1985;13(19);7025-39. PMID: 2997734

Neuwald89: Neuwald AF, Stauffer GV (1989). "An Escherichia coli membrane protein with a unique signal sequence." Gene 1989;82(2);219-28. PMID: 2684780

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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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